# # Authors: F.-Y. Dupradeau & P. Cieplak # http://upjv.q4md-forcefieldtools.org/ # # Force field topology database (FFTopDB) generated using R.E.D.-IV # 28 building blocks used in the fit (molecular orientations & conformations for each molecule fully defined). # 89 molecular fragments generated allowing the construction of many libraries for biochemical cofactors... # # (1) Fragments available in R.E.DD.B. # (2) Files generated by R.E.D.-IV # (3) Fragment description # (4) Fragment names in the FFTopDB # # (1) (2) (3) (4) # tripos1.mol2 mm1-o1.FG1.mol2 Fragment "O-PO2(-)-O-PO2(-)-O" POP # tripos2.mol2 mm2-o1-FG2.mol2 Fragment "O-PO2(-)" P1 # tripos3.mol2 mm2-o1-FG3.mol2 Fragment "O-PO2(-)-OH" P1M # tripos4.mol2 mm3-o1-FG1.mol2 Fragment "O-PO2(-)-O(-)" P2M # tripos5.mol2 mm4-o1.mol2 2-Deoxy-Adenosine AN # tripos6.mol2 mm4-o1.FG1.mol2 Fragment "2-Deoxy-Adenosine - (HO5' HO3')" AC # tripos7.mol2 mm4-o1.FG3.mol2 Fragment "2-Deoxy-Adenosine - (HO5')" A5 # tripos8.mol2 mm4-o1.FG4.mol2 Fragment "2-Deoxy-Adenosine - (HO3')" A3 # tripos9.mol2 mm5-o1.mol2 2-Deoxy-Cytidine CN # tripos10.mol2 mm5-o1.FG1.mol2 Fragment "2-Deoxy-Cytidine - (HO5' HO3')" CC # tripos11.mol2 mm5-o1.FG3.mol2 Fragment "2-Deoxy-Cytidine - (HO5')" C5 # tripos12.mol2 mm5-o1.FG4.mol2 Fragment "2-Deoxy-Cytidine - (HO3')" C3 # tripos13.mol2 mm6-o1.mol2 2-Deoxy-Guanosine GN # tripos14.mol2 mm6-o1.FG1.mol2 Fragment "2-Deoxy-Guanosine - (HO5' HO3')" GC # tripos15.mol2 mm6-o1.FG3.mol2 Fragment "2-Deoxy-Guanosine - (HO5')" G5 # tripos16.mol2 mm6-o1.FG4.mol2 Fragment "2-Deoxy-Guanosine - (HO3')" G3 # tripos17.mol2 mm7-o1.mol2 2-Deoxy-Thymidine TN # tripos18.mol2 mm7-o1.FG1.mol2 Fragment "2-Deoxy-Thymidine - (HO5' HO3')" TC # tripos19.mol2 mm7-o1.FG3.mol2 Fragment "2-Deoxy-Thymidine - (HO5')" T5 # tripos20.mol2 mm7-o1.FG4.mol2 Fragment "2-Deoxy-Thymidine - (HO3')" T3 # tripos21.mol2 mm8-o1.mol2 Adenosine BN # tripos22.mol2 mm8-o1.FG1.mol2 Fragment "Adenosine - (HO5' HO3' HO2')" BC # tripos23.mol2 mm8-o1.FG3.mol2 Fragment "Adenosine - (HO5')" B5 # tripos24.mol2 mm8-o1.FG4.mol2 Fragment "Adenosine - (HO3')" B3 # tripos25.mol2 mm8-o1.FG5.mol2 Fragment "Adenosine - (HO2')" B2 # tripos26.mol2 mm8-o1.FG6.mol2 Fragment "Adenosine - (HO5' HO3')" B53 # tripos27.mol2 mm8-o1.FG7.mol2 Fragment "Adenosine - (HO5' HO2')" B52 # tripos28.mol2 mm8-o1.FG8.mol2 Fragment "Adenosine - (HO3' HO2')" B32 # tripos29.mol2 mm9-o1.mol2 Cytidine DN # tripos30.mol2 mm9-o1.FG1.mol2 Fragment "Cytidine - (HO5' HO3' HO2')" DC # tripos31.mol2 mm9-o1.FG3.mol2 Fragment "Cytidine - (HO5')" D5 # tripos32.mol2 mm9-o1.FG4.mol2 Fragment "Cytidine - (HO3')" D3 # tripos33.mol2 mm9-o1.FG5.mol2 Fragment "Cytidine - (HO2')" D2 # tripos34.mol2 mm9-o1.FG6.mol2 Fragment "Cytidine - (HO5' HO3')" D53 # tripos35.mol2 mm9-o1.FG7.mol2 Fragment "Cytidine - (HO5' HO2')" D52 # tripos36.mol2 mm9-o1.FG8.mol2 Fragment "Cytidine - (HO3' HO2')" D32 # tripos37.mol2 mm10-o1.mol2 Guanosine HN # tripos38.mol2 mm10-o1.FG1.mol2 Fragment "Guanosine - (HO5' HO3' HO2')" HC # tripos39.mol2 mm10-o1.FG3.mol2 Fragment "Guanosine - (HO5')" H5 # tripos40.mol2 mm10-o1.FG4.mol2 Fragment "Guanosine - (HO3')" H3 # tripos41.mol2 mm10-o1.FG5.mol2 Fragment "Guanosine - (HO2')" H2 # tripos42.mol2 mm10-o1.FG6.mol2 Fragment "Guanosine - (HO5' HO3')" H53 # tripos43.mol2 mm10-o1.FG7.mol2 Fragment "Guanosine - (HO5' HO2')" H52 # tripos44.mol2 mm10-o1.FG8.mol2 Fragment "Guanosine - (HO3' HO2')" H32 # tripos45.mol2 mm11-o1.mol2 Uridine UN # tripos46.mol2 mm11-o1.FG1.mol2 Fragment "Uridine - (HO5' HO3' HO2')" UC # tripos47.mol2 mm11-o1.FG3.mol2 Fragment "Uridine - (HO5')" U5 # tripos48.mol2 mm11-o1.FG4.mol2 Fragment "Uridine - (HO3')" U3 # tripos49.mol2 mm11-o1.FG5.mol2 Fragment "Uridine - (HO2')" U2 # tripos50.mol2 mm11-o1.FG6.mol2 Fragment "Uridine - (HO5' HO3')" U53 # tripos51.mol2 mm11-o1.FG7.mol2 Fragment "Uridine - (HO5' HO2')" U52 # tripos52.mol2 mm11-o1.FG8.mol2 Fragment "Uridine - (HO3' HO2')" U32 # tripos53.mol2 mm12-o1.mol2 1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide RN # tripos54.mol2 mm12-o1.FG1.mol2 Fragment "1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide - (HO5' HO3' HO2')" RC # tripos55.mol2 mm12-o1.FG3.mol2 Fragment "1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide - (HO5')" R5 # tripos56.mol2 mm12-o1.FG4.mol2 Fragment "1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide - (HO3')" R3 # tripos57.mol2 mm12-o1.FG5.mol2 Fragment "1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide - (HO2')" R2 # tripos58.mol2 mm12-o1.FG6.mol2 Fragment "1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide - (HO5' HO3')" R53 # tripos59.mol2 mm12-o1.FG7.mol2 Fragment "1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide - (HO5' HO2')" R52 # tripos60.mol2 mm12-o1.FG8.mol2 Fragment "1-D-ribofuranosyl-1,4-dihydropyridine-3-carboxamide - (HO3' HO2')" R32 # tripos61.mol2 mm13-o1.mol2 3-(aminocarbonyl)-1-D-ribofuranosylpyridinium IN # tripos62.mol2 mm13-o1.FG1.mol2 Fragment "3-(aminocarbonyl)-1-D-ribofuranosylpyridinium - (HO5' HO3' HO2')" IC # tripos63.mol2 mm13-o1.FG3.mol2 Fragment "3-(aminocarbonyl)-1-D-ribofuranosylpyridinium - (HO5')" I5 # tripos64.mol2 mm13-o1.FG4.mol2 Fragment "3-(aminocarbonyl)-1-D-ribofuranosylpyridinium - (HO3')" I3 # tripos65.mol2 mm13-o1.FG5.mol2 Fragment "3-(aminocarbonyl)-1-D-ribofuranosylpyridinium - (HO2')" I2 # tripos66.mol2 mm13-o1.FG6.mol2 Fragment "3-(aminocarbonyl)-1-D-ribofuranosylpyridinium - (HO5' HO3')" I53 # tripos67.mol2 mm13-o1.FG7.mol2 Fragment "3-(aminocarbonyl)-1-D-ribofuranosylpyridinium - (HO5' HO2')" I52 # tripos68.mol2 mm13-o1.FG8.mol2 Fragment "3-(aminocarbonyl)-1-D-ribofuranosylpyridinium - (HO3' HO2')" I32 # tripos69.mol2 mm14-o1.FG1.mol2 Fragment "(2S,3S,4R)-1-amino-1-deoxypentitol - (NH2 OH)" LNK # tripos70.mol2 mm14-o1.FG3.mol2 Fragment "(2S,3S,4R)-1-amino-1-deoxypentitol - (NH2)" LNO # tripos71.mol2 mm15-o1.FG1.mol2 Fragment "7,8,10-trimethylbenzo[g]pteridine-2,4(3H,10H)-dione - (Me)" FLO # tripos72.mol2 mm16-o1.FG1.mol2 Fragment "7,8,10-trimethyl-5,10-dihydrobenzo[g]pteridine-2,4(1H,3H)-dione - (Me)" FLR # tripos73.mol2 mm17-o1.FG1.mol2 Fragment "(2R)-2,4-dihydroxy-N,3,3-trimethylbutanamide - (OH NHMe)" AC1 # tripos74.mol2 mm17-o1.FG3.mol2 Fragment "(2R)-2,4-dihydroxy-N,3,3-trimethylbutanamide - (NHMe)" AO1 # tripos75.mol2 mm18-o1.FG1.mol2 Fragment "N3-acetyl-N-methyl-b-alaninamide -(MeCO NHMe)" AC2 # tripos76.mol2 mm19-o1.FG1.mol2 Fragment "S-[2-(acetylamino)ethyl]-ethanethioate (MeCO)" AC3 # tripos77.mol2 mm20-o1.FG1.mol2 Fragment "N-(2-sulfanylethyl)acetamide - (MeCO)" AC4 # tripos78.mol2 mm21-o1.mol2 2-deoxy-cyclic-AMP CAP # tripos79.mol2 mm22-o1.mol2 2-deoxy-cyclic-CMP CCP # tripos80.mol2 mm23-o1.mol2 2-deoxy-cyclic-GMP CGP # tripos81.mol2 mm24-o1.mol2 2-deoxy-cyclic-TMP CTP # tripos82.mol2 mm25-o1.mol2 cyclic-AMP CBP # tripos83.mol2 mm25-o1.FG1.mol2 Fragment "cyclic-AMP - (HO2')" CBO # tripos84.mol2 mm26-o1.mol2 cyclic-CMP CDP # tripos85.mol2 mm26-o1.FG1.mol2 Fragment "cyclic-CMP - (HO2')" CDO # tripos86.mol2 mm27-o1.mol2 cyclic-GMP CHP # tripos87.mol2 mm27-o1.FG1.mol2 Fragment "cyclic-GMP - (HO2')" CHO # tripos88.mol2 mm28-o1.mol2 cyclic-UMP CUP # tripos89.mol2 mm28-o1.FG1.mol2 Fragment "cyclic-UMP - (HO2')" CUO # logFile leap_q4md-forcefieldtools.log alias e edit alias q quit alias c charge alias mg measuregeom alias i impose alias seq sequence ########## Activate the 89 lines below: perl -p -i.old -e 's/\#\#\!\# //g' script1.ff ##!# POP = loadmol2 ./tripos1.mol2 ##!# P1 = loadmol2 ./tripos2.mol2 ##!# P1M = loadmol2 ./tripos3.mol2 ##!# P2M = loadmol2 ./tripos4.mol2 ##!# AN = loadmol2 ./tripos5.mol2 ##!# AC = loadmol2 ./tripos6.mol2 ##!# A5 = loadmol2 ./tripos7.mol2 ##!# A3 = loadmol2 ./tripos8.mol2 ##!# CN = loadmol2 ./tripos9.mol2 ##!# CC = loadmol2 ./tripos10.mol2 ##!# C5 = loadmol2 ./tripos11.mol2 ##!# C3 = loadmol2 ./tripos12.mol2 ##!# GN = loadmol2 ./tripos13.mol2 ##!# GC = loadmol2 ./tripos14.mol2 ##!# G5 = loadmol2 ./tripos15.mol2 ##!# G3 = loadmol2 ./tripos16.mol2 ##!# TN = loadmol2 ./tripos17.mol2 ##!# TC = loadmol2 ./tripos18.mol2 ##!# T5 = loadmol2 ./tripos19.mol2 ##!# T3 = loadmol2 ./tripos20.mol2 ##!# BN = loadmol2 ./tripos21.mol2 ##!# BC = loadmol2 ./tripos22.mol2 ##!# B5 = loadmol2 ./tripos23.mol2 ##!# B3 = loadmol2 ./tripos24.mol2 ##!# B2 = loadmol2 ./tripos25.mol2 ##!# B53 = loadmol2 ./tripos26.mol2 ##!# B52 = loadmol2 ./tripos27.mol2 ##!# B32 = loadmol2 ./tripos28.mol2 ##!# DN = loadmol2 ./tripos29.mol2 ##!# DC = loadmol2 ./tripos30.mol2 ##!# D5 = loadmol2 ./tripos31.mol2 ##!# D3 = loadmol2 ./tripos32.mol2 ##!# D2 = loadmol2 ./tripos33.mol2 ##!# D53 = loadmol2 ./tripos34.mol2 ##!# D52 = loadmol2 ./tripos35.mol2 ##!# D32 = loadmol2 ./tripos36.mol2 ##!# HN = loadmol2 ./tripos37.mol2 ##!# HC = loadmol2 ./tripos38.mol2 ##!# H5 = loadmol2 ./tripos39.mol2 ##!# H3 = loadmol2 ./tripos40.mol2 ##!# H2 = loadmol2 ./tripos41.mol2 ##!# H53 = loadmol2 ./tripos42.mol2 ##!# H52 = loadmol2 ./tripos43.mol2 ##!# H32 = loadmol2 ./tripos44.mol2 ##!# UN = loadmol2 ./tripos45.mol2 ##!# UC = loadmol2 ./tripos46.mol2 ##!# U5 = loadmol2 ./tripos47.mol2 ##!# U3 = loadmol2 ./tripos48.mol2 ##!# U2 = loadmol2 ./tripos49.mol2 ##!# U53 = loadmol2 ./tripos50.mol2 ##!# U52 = loadmol2 ./tripos51.mol2 ##!# U32 = loadmol2 ./tripos52.mol2 ##!# RN = loadmol2 ./tripos53.mol2 ##!# RC = loadmol2 ./tripos54.mol2 ##!# R5 = loadmol2 ./tripos55.mol2 ##!# R3 = loadmol2 ./tripos56.mol2 ##!# R2 = loadmol2 ./tripos57.mol2 ##!# R53 = loadmol2 ./tripos58.mol2 ##!# R52 = loadmol2 ./tripos59.mol2 ##!# R32 = loadmol2 ./tripos60.mol2 ##!# IN = loadmol2 ./tripos61.mol2 ##!# IC = loadmol2 ./tripos62.mol2 ##!# I5 = loadmol2 ./tripos63.mol2 ##!# I3 = loadmol2 ./tripos64.mol2 ##!# I2 = loadmol2 ./tripos65.mol2 ##!# I53 = loadmol2 ./tripos66.mol2 ##!# I52 = loadmol2 ./tripos67.mol2 ##!# I32 = loadmol2 ./tripos68.mol2 ##!# LNK = loadmol2 ./tripos69.mol2 ##!# LNO = loadmol2 ./tripos70.mol2 ##!# FLO = loadmol2 ./tripos71.mol2 ##!# FLR = loadmol2 ./tripos72.mol2 ##!# AC1 = loadmol2 ./tripos73.mol2 ##!# AO1 = loadmol2 ./tripos74.mol2 ##!# AC2 = loadmol2 ./tripos75.mol2 ##!# AC3 = loadmol2 ./tripos76.mol2 ##!# AC4 = loadmol2 ./tripos77.mol2 ##!# CAP = loadmol2 ./tripos78.mol2 ##!# CCP = loadmol2 ./tripos79.mol2 ##!# CGP = loadmol2 ./tripos80.mol2 ##!# CTP = loadmol2 ./tripos81.mol2 ##!# CBP = loadmol2 ./tripos82.mol2 ##!# CBO = loadmol2 ./tripos83.mol2 ##!# CDP = loadmol2 ./tripos84.mol2 ##!# CDO = loadmol2 ./tripos85.mol2 ##!# CHP = loadmol2 ./tripos86.mol2 ##!# CHO = loadmol2 ./tripos87.mol2 ##!# CUP = loadmol2 ./tripos88.mol2 ##!# CUO = loadmol2 ./tripos89.mol2 ########## Remove the 89 lines below: grep -v "to be replaced by the correct tripos" script1.ff > script1-new.ff POP = loadmol2 ./mm1-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file P1 = loadmol2 ./mm2-o1.FG2.mol2 # to be replaced by the correct tripos$n.mol2 file P1M = loadmol2 ./mm2-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file P2M = loadmol2 ./mm3-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file AN = loadmol2 ./mm4-o1.mol2 # to be replaced by the correct tripos$n.mol2 file AC = loadmol2 ./mm4-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file A5 = loadmol2 ./mm4-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file A3 = loadmol2 ./mm4-o1.FG4.mol2 # to be replaced by the correct tripos$n.mol2 file CN = loadmol2 ./mm5-o1.mol2 # to be replaced by the correct tripos$n.mol2 file CC = loadmol2 ./mm5-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file C5 = loadmol2 ./mm5-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file C3 = loadmol2 ./mm5-o1.FG4.mol2 # to be replaced by the correct tripos$n.mol2 file GN = loadmol2 ./mm6-o1.mol2 # to be replaced by the correct tripos$n.mol2 file GC = loadmol2 ./mm6-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file G5 = loadmol2 ./mm6-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file G3 = loadmol2 ./mm6-o1.FG4.mol2 # to be replaced by the correct tripos$n.mol2 file TN = loadmol2 ./mm7-o1.mol2 # to be replaced by the correct tripos$n.mol2 file TC = loadmol2 ./mm7-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file T5 = loadmol2 ./mm7-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file T3 = loadmol2 ./mm7-o1.FG4.mol2 # to be replaced by the correct tripos$n.mol2 file BN = loadmol2 ./mm8-o1.mol2 # to be replaced by the correct tripos$n.mol2 file BC = loadmol2 ./mm8-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file B5 = loadmol2 ./mm8-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file B3 = loadmol2 ./mm8-o1.FG4.mol2 # to be replaced by the correct tripos$n.mol2 file B2 = loadmol2 ./mm8-o1.FG5.mol2 # to be replaced by the correct tripos$n.mol2 file B53 = loadmol2 ./mm8-o1.FG6.mol2 # to be replaced by the correct tripos$n.mol2 file B52 = loadmol2 ./mm8-o1.FG7.mol2 # to be replaced by the correct tripos$n.mol2 file B32 = loadmol2 ./mm8-o1.FG8.mol2 # to be replaced by the correct tripos$n.mol2 file DN = loadmol2 ./mm9-o1.mol2 # to be replaced by the correct tripos$n.mol2 file DC = loadmol2 ./mm9-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file D5 = loadmol2 ./mm9-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file D3 = loadmol2 ./mm9-o1.FG4.mol2 # to be replaced by the correct tripos$n.mol2 file D2 = loadmol2 ./mm9-o1.FG5.mol2 # to be replaced by the correct tripos$n.mol2 file D53 = loadmol2 ./mm9-o1.FG6.mol2 # to be replaced by the correct tripos$n.mol2 file D52 = loadmol2 ./mm9-o1.FG7.mol2 # to be replaced by the correct tripos$n.mol2 file D32 = loadmol2 ./mm9-o1.FG8.mol2 # to be replaced by the correct tripos$n.mol2 file HN = loadmol2 ./mm10-o1.mol2 # to be replaced by the correct tripos$n.mol2 file HC = loadmol2 ./mm10-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file H5 = loadmol2 ./mm10-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file H3 = loadmol2 ./mm10-o1.FG4.mol2 # to be replaced by the correct tripos$n.mol2 file H2 = loadmol2 ./mm10-o1.FG5.mol2 # to be replaced by the correct tripos$n.mol2 file H53 = loadmol2 ./mm10-o1.FG6.mol2 # to be replaced by the correct tripos$n.mol2 file H52 = loadmol2 ./mm10-o1.FG7.mol2 # to be replaced by the correct tripos$n.mol2 file H32 = loadmol2 ./mm10-o1.FG8.mol2 # to be replaced by the correct tripos$n.mol2 file UN = loadmol2 ./mm11-o1.mol2 # to be replaced by the correct tripos$n.mol2 file UC = loadmol2 ./mm11-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file U5 = loadmol2 ./mm11-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file U3 = loadmol2 ./mm11-o1.FG4.mol2 # to be replaced by the correct tripos$n.mol2 file U2 = loadmol2 ./mm11-o1.FG5.mol2 # to be replaced by the correct tripos$n.mol2 file U53 = loadmol2 ./mm11-o1.FG6.mol2 # to be replaced by the correct tripos$n.mol2 file U52 = loadmol2 ./mm11-o1.FG7.mol2 # to be replaced by the correct tripos$n.mol2 file U32 = loadmol2 ./mm11-o1.FG8.mol2 # to be replaced by the correct tripos$n.mol2 file RN = loadmol2 ./mm12-o1.mol2 # to be replaced by the correct tripos$n.mol2 file RC = loadmol2 ./mm12-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file R5 = loadmol2 ./mm12-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file R3 = loadmol2 ./mm12-o1.FG4.mol2 # to be replaced by the correct tripos$n.mol2 file R2 = loadmol2 ./mm12-o1.FG5.mol2 # to be replaced by the correct tripos$n.mol2 file R53 = loadmol2 ./mm12-o1.FG6.mol2 # to be replaced by the correct tripos$n.mol2 file R52 = loadmol2 ./mm12-o1.FG7.mol2 # to be replaced by the correct tripos$n.mol2 file R32 = loadmol2 ./mm12-o1.FG8.mol2 # to be replaced by the correct tripos$n.mol2 file IN = loadmol2 ./mm13-o1.mol2 # to be replaced by the correct tripos$n.mol2 file IC = loadmol2 ./mm13-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file I5 = loadmol2 ./mm13-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file I3 = loadmol2 ./mm13-o1.FG4.mol2 # to be replaced by the correct tripos$n.mol2 file I2 = loadmol2 ./mm13-o1.FG5.mol2 # to be replaced by the correct tripos$n.mol2 file I53 = loadmol2 ./mm13-o1.FG6.mol2 # to be replaced by the correct tripos$n.mol2 file I52 = loadmol2 ./mm13-o1.FG7.mol2 # to be replaced by the correct tripos$n.mol2 file I32 = loadmol2 ./mm13-o1.FG8.mol2 # to be replaced by the correct tripos$n.mol2 file LNK = loadmol2 ./mm14-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file LNO = loadmol2 ./mm14-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file FLO = loadmol2 ./mm15-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file FLR = loadmol2 ./mm16-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file AC1 = loadmol2 ./mm17-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file AO1 = loadmol2 ./mm17-o1.FG3.mol2 # to be replaced by the correct tripos$n.mol2 file AC2 = loadmol2 ./mm18-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file AC3 = loadmol2 ./mm19-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file AC4 = loadmol2 ./mm20-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file CAP = loadmol2 ./mm21-o1.mol2 # to be replaced by the correct tripos$n.mol2 file CCP = loadmol2 ./mm22-o1.mol2 # to be replaced by the correct tripos$n.mol2 file CGP = loadmol2 ./mm23-o1.mol2 # to be replaced by the correct tripos$n.mol2 file CTP = loadmol2 ./mm24-o1.mol2 # to be replaced by the correct tripos$n.mol2 file CBP = loadmol2 ./mm25-o1.mol2 # to be replaced by the correct tripos$n.mol2 file CBO = loadmol2 ./mm25-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file CDP = loadmol2 ./mm26-o1.mol2 # to be replaced by the correct tripos$n.mol2 file CDO = loadmol2 ./mm26-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file CHP = loadmol2 ./mm27-o1.mol2 # to be replaced by the correct tripos$n.mol2 file CHO = loadmol2 ./mm27-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file CUP = loadmol2 ./mm28-o1.mol2 # to be replaced by the correct tripos$n.mol2 file CUO = loadmol2 ./mm28-o1.FG1.mol2 # to be replaced by the correct tripos$n.mol2 file verbosity 2 addAtomTypes { { "H" "H" "sp3" } { "HO" "H" "sp3" } { "HS" "H" "sp3" } { "H1" "H" "sp3" } { "H2" "H" "sp3" } { "H3" "H" "sp3" } { "H4" "H" "sp3" } { "H5" "H" "sp3" } { "HW" "H" "sp3" } { "HC" "H" "sp3" } { "HA" "H" "sp3" } { "HP" "H" "sp3" } { "OH" "O" "sp3" } { "OS" "O" "sp3" } { "O" "O" "sp2" } { "O2" "O" "sp2" } { "OW" "O" "sp3" } { "CT" "C" "sp3" } { "CH" "C" "sp3" } { "C2" "C" "sp3" } { "C3" "C" "sp3" } { "C" "C" "sp2" } { "C*" "C" "sp2" } { "CA" "C" "sp2" } { "CB" "C" "sp2" } { "CC" "C" "sp2" } { "CN" "C" "sp2" } { "CM" "C" "sp2" } { "CK" "C" "sp2" } { "CQ" "C" "sp2" } { "CD" "C" "sp2" } { "CE" "C" "sp2" } { "CF" "C" "sp2" } { "CP" "C" "sp2" } { "CI" "C" "sp2" } { "CJ" "C" "sp2" } { "CW" "C" "sp2" } { "CV" "C" "sp2" } { "CR" "C" "sp2" } { "CA" "C" "sp2" } { "CY" "C" "sp2" } { "C0" "C" "sp2" } { "MG" "Mg" "sp3" } { "N" "N" "sp2" } { "NA" "N" "sp2" } { "N2" "N" "sp2" } { "N*" "N" "sp2" } { "NP" "N" "sp2" } { "NQ" "N" "sp2" } { "NB" "N" "sp2" } { "NC" "N" "sp2" } { "NT" "N" "sp3" } { "N3" "N" "sp3" } { "S" "S" "sp3" } { "SH" "S" "sp3" } { "P" "P" "sp3" } } # Add your own atom types if required... # addAtomTypes { # # } parm99 = loadamberparams parm99.dat frcmod99SB = loadamberparams frcmod.ff99SB FRCMOD = loadamberparams script3.ff # loadOff all_nucleic94.lib loadOff ions94.lib loadOff solvents.lib HOH = TP3 WAT = TP3 set POP name "POP" set POP head POP.1.O5A set POP tail POP.1.O5B set POP.1 connect0 POP.1.O5A set POP.1 connect1 POP.1.O5B set POP.1 restype undefined set POP.1 name "POP" # set FF atom types set POP.1.O5A type OS set POP.1.PA type P set POP.1.OA1 type O2 set POP.1.OA2 type O2 set POP.1.OP type OS set POP.1.PB type P set POP.1.OB1 type O2 set POP.1.OB2 type O2 set POP.1.O5B type OS set P1 name "P1" set P1 head P1.1.P set P1 tail P1.1.OR set P1.1 connect0 P1.1.P set P1.1 connect1 P1.1.OR set P1.1 restype undefined set P1.1 name "P1" # set FF atom types set P1.1.OR type OS set P1.1.P type P set P1.1.OP1 type O2 set P1.1.OP2 type O2 set P1M name "P1M" # head null set P1M tail P1M.1.OR set P1M.1 connect0 P1M.1.P set P1M.1 connect1 P1M.1.OR set P1M.1 restype undefined set P1M.1 name "P1M" # set FF atom types set P1M.1.OR type OS set P1M.1.P type P set P1M.1.OP1 type O2 set P1M.1.OP2 type O2 set P1M.1.OH type OH set P1M.1.HO type HO set P2M name "P2M" # head null set P2M tail P2M.1.OR set P2M.1 connect0 P2M.1.P set P2M.1 connect1 P2M.1.OR set P2M.1 restype undefined set P2M.1 name "P2M" # set FF atom types set P2M.1.OR type OS set P2M.1.P type P set P2M.1.OP1 type O2 set P2M.1.OP2 type O2 set P2M.1.OP3 type O2 # ------- 2-deoxy-adenosine nucleoside fragments ----------- set AN name "AN" # head & tail null set AN.1 connect0 AN.1.C5' set AN.1 connect1 AN.1.C2' set AN.1 restype nucleic set AN.1 name "AN" # set FF atom types set AN.1.O5' type OH set AN.1.H5T type HO set AN.1.O3' type OH set AN.1.H3T type HO set AN.1.C5' type CT set AN.1.H5'1 type H1 set AN.1.H5'2 type H1 set AN.1.O4' type OS set AN.1.C4' type CT set AN.1.H4' type H1 set AN.1.C3' type CT set AN.1.H3' type H1 set AN.1.C2' type CT set AN.1.H2'1 type "HC" set AN.1.H2'2 type "HC" set AN.1.C1' type CT set AN.1.H1' type "H2" set AN.1.N6 type N2 set AN.1.H61 type H set AN.1.H62 type H set AN.1.C6 type CA set AN.1.C5 type CB set AN.1.N7 type NB set AN.1.C8 type CK set AN.1.H8 type "H5" set AN.1.N9 type "N*" set AN.1.C4 type CB set AN.1.N3 type NC set AN.1.C2 type CQ set AN.1.H2 type "H5" set AN.1.N1 type NC set AC name "AC" set AC head AC.1.C5' set AC tail AC.1.C2' set AC.1 connect0 AC.1.C5' set AC.1 connect1 AC.1.C2' set AC.1 restype nucleic set AC.1 name "AC" # set FF atom types set AC.1.C5' type CT set AC.1.H5'1 type H1 set AC.1.H5'2 type H1 set AC.1.O4' type OS set AC.1.C4' type CT set AC.1.H4' type H1 set AC.1.C3' type CT set AC.1.H3' type H1 set AC.1.C2' type CT set AC.1.H2'1 type "HC" set AC.1.H2'2 type "HC" set AC.1.C1' type CT set AC.1.H1' type "H2" set AC.1.N6 type N2 set AC.1.H61 type H set AC.1.H62 type H set AC.1.C6 type CA set AC.1.C5 type CB set AC.1.N7 type NB set AC.1.C8 type CK set AC.1.H8 type "H5" set AC.1.N9 type "N*" set AC.1.C4 type CB set AC.1.N3 type NC set AC.1.C2 type CQ set AC.1.H2 type "H5" set AC.1.N1 type NC set A5 name "A5" set A5 head A5.1.C5' # tail null set A5.1 connect0 A5.1.C5' set A5.1 connect1 A5.1.C2' set A5.1 restype nucleic set A5.1 name "A5" # set FF atom types set A5.1.O3' type OH set A5.1.H3T type HO set A5.1.C5' type CT set A5.1.H5'1 type H1 set A5.1.H5'2 type H1 set A5.1.O4' type OS set A5.1.C4' type CT set A5.1.H4' type H1 set A5.1.C3' type CT set A5.1.H3' type H1 set A5.1.C2' type CT set A5.1.H2'1 type "HC" set A5.1.H2'2 type "HC" set A5.1.C1' type CT set A5.1.H1' type "H2" set A5.1.N6 type N2 set A5.1.H61 type H set A5.1.H62 type H set A5.1.C6 type CA set A5.1.C5 type CB set A5.1.N7 type NB set A5.1.C8 type CK set A5.1.H8 type "H5" set A5.1.N9 type "N*" set A5.1.C4 type CB set A5.1.N3 type NC set A5.1.C2 type CQ set A5.1.H2 type "H5" set A5.1.N1 type NC set A3 name "A3" set A3 head A3.1.C3' # tail null set A3.1 connect0 A3.1.C3' set A3.1 connect1 A3.1.C2' set A3.1 restype nucleic set A3.1 name "A3" # set FF atom types set A3.1.O5' type OH set A3.1.H5T type HO set A3.1.C5' type CT set A3.1.H5'1 type H1 set A3.1.H5'2 type H1 set A3.1.O4' type OS set A3.1.C4' type CT set A3.1.H4' type H1 set A3.1.C3' type CT set A3.1.H3' type H1 set A3.1.C2' type CT set A3.1.H2'1 type "HC" set A3.1.H2'2 type "HC" set A3.1.C1' type CT set A3.1.H1' type "H2" set A3.1.N6 type N2 set A3.1.H61 type H set A3.1.H62 type H set A3.1.C6 type CA set A3.1.C5 type CB set A3.1.N7 type NB set A3.1.C8 type CK set A3.1.H8 type "H5" set A3.1.N9 type "N*" set A3.1.C4 type CB set A3.1.N3 type NC set A3.1.C2 type CQ set A3.1.H2 type "H5" set A3.1.N1 type NC # ------- 2-deoxy-cystosine nucleoside fragments ----------- set CN name "CN" # head & tail null set CN.1 connect0 CN.1.C5' set CN.1 connect1 CN.1.C2' set CN.1 restype nucleic set CN.1 name "CN" # set FF atom types set CN.1.O5' type OH set CN.1.H5T type HO set CN.1.O3' type OH set CN.1.H3T type HO set CN.1.C5' type CT set CN.1.H5'1 type H1 set CN.1.H5'2 type H1 set CN.1.O4' type OS set CN.1.C4' type CT set CN.1.H4' type H1 set CN.1.C3' type CT set CN.1.H3' type H1 set CN.1.C2' type CT set CN.1.H2'1 type "HC" set CN.1.H2'2 type "HC" set CN.1.C1' type CT set CN.1.H1' type "H2" set CN.1.N4 type N2 set CN.1.H41 type H set CN.1.H42 type H set CN.1.C4 type CA set CN.1.N3 type NC set CN.1.C2 type C set CN.1.O2 type O set CN.1.N1 type "N*" set CN.1.C6 type CM set CN.1.H6 type H4 set CN.1.C5 type CM set CN.1.H5 type HA set CC name "CC" set CC head CC.1.C5' set CC tail CC.1.C2' set CC.1 connect0 CC.1.C5' set CC.1 connect1 CC.1.C2' set CC.1 restype nucleic set CC.1 name "CC" # set FF atom types set CC.1.C5' type CT set CC.1.H5'1 type H1 set CC.1.H5'2 type H1 set CC.1.O4' type OS set CC.1.C4' type CT set CC.1.H4' type H1 set CC.1.C3' type CT set CC.1.H3' type H1 set CC.1.C2' type CT set CC.1.H2'1 type "HC" set CC.1.H2'2 type "HC" set CC.1.C1' type CT set CC.1.H1' type "H2" set CC.1.N4 type N2 set CC.1.H41 type H set CC.1.H42 type H set CC.1.C4 type CA set CC.1.N3 type NC set CC.1.C2 type C set CC.1.O2 type O set CC.1.N1 type "N*" set CC.1.C6 type CM set CC.1.H6 type H4 set CC.1.C5 type CM set CC.1.H5 type HA set C5 name "C5" set C5 head C5.1.C5' # tail null set C5.1 connect0 C5.1.C5' set C5.1 connect1 C5.1.C2' set C5.1 restype nucleic set C5.1 name "C5" # set FF atom types set C5.1.O3' type OH set C5.1.H3T type HO set C5.1.C5' type CT set C5.1.H5'1 type H1 set C5.1.H5'2 type H1 set C5.1.O4' type OS set C5.1.C4' type CT set C5.1.H4' type H1 set C5.1.C3' type CT set C5.1.H3' type H1 set C5.1.C2' type CT set C5.1.H2'1 type "HC" set C5.1.H2'2 type "HC" set C5.1.C1' type CT set C5.1.H1' type "H2" set C5.1.N4 type N2 set C5.1.H41 type H set C5.1.H42 type H set C5.1.C4 type CA set C5.1.N3 type NC set C5.1.C2 type C set C5.1.O2 type O set C5.1.N1 type "N*" set C5.1.C6 type CM set C5.1.H6 type H4 set C5.1.C5 type CM set C5.1.H5 type HA set C3 name "C3" set C3 head C3.1.C3' # tail null set C3.1 connect0 C3.1.C3' set C3.1 connect1 C3.1.C2' set C3.1 restype nucleic set C3.1 name "C3" # set FF atom types set C3.1.O5' type OH set C3.1.H5T type HO set C3.1.C5' type CT set C3.1.H5'1 type H1 set C3.1.H5'2 type H1 set C3.1.O4' type OS set C3.1.C4' type CT set C3.1.H4' type H1 set C3.1.C3' type CT set C3.1.H3' type H1 set C3.1.C2' type CT set C3.1.H2'1 type "HC" set C3.1.H2'2 type "HC" set C3.1.C1' type CT set C3.1.H1' type "H2" set C3.1.N4 type N2 set C3.1.H41 type H set C3.1.H42 type H set C3.1.C4 type CA set C3.1.N3 type NC set C3.1.C2 type C set C3.1.O2 type O set C3.1.N1 type "N*" set C3.1.C6 type CM set C3.1.H6 type H4 set C3.1.C5 type CM set C3.1.H5 type HA # ------- 2-deoy-guanosine nucleoside fragments ----------- set GN name "GN" # head & tail null set GN.1 connect0 GN.1.C5' set GN.1 connect1 GN.1.C2' set GN.1 restype nucleic set GN.1 name "GN" # set FF atom types set GN.1.O5' type OH set GN.1.H5T type HO set GN.1.O3' type OH set GN.1.H3T type HO set GN.1.C5' type CT set GN.1.H5'1 type H1 set GN.1.H5'2 type H1 set GN.1.O4' type OS set GN.1.C4' type CT set GN.1.H4' type H1 set GN.1.C3' type CT set GN.1.H3' type H1 set GN.1.C2' type CT set GN.1.H2'1 type "HC" set GN.1.H2'2 type "HC" set GN.1.C1' type CT set GN.1.H1' type "H2" set GN.1.N2 type N2 set GN.1.H21 type H set GN.1.H22 type H set GN.1.O6 type O set GN.1.C6 type C set GN.1.C5 type CB set GN.1.N7 type NB set GN.1.C8 type CK set GN.1.H8 type "H5" set GN.1.N9 type "N*" set GN.1.C4 type CB set GN.1.N3 type NC set GN.1.C2 type CA set GN.1.N1 type NA set GN.1.H1 type H set GC name "GC" set GC head GC.1.C5' set GC tail GC.1.C2' set GC.1 connect0 GC.1.C5' set GC.1 connect1 GC.1.C2' set GC.1 restype nucleic set GC.1 name "GC" # set FF atom types set GC.1.C5' type CT set GC.1.H5'1 type H1 set GC.1.H5'2 type H1 set GC.1.O4' type OS set GC.1.C4' type CT set GC.1.H4' type H1 set GC.1.C3' type CT set GC.1.H3' type H1 set GC.1.C2' type CT set GC.1.H2'1 type "HC" set GC.1.H2'2 type "HC" set GC.1.C1' type CT set GC.1.H1' type "H2" set GC.1.N2 type N2 set GC.1.H21 type H set GC.1.H22 type H set GC.1.O6 type O set GC.1.C6 type C set GC.1.C5 type CB set GC.1.N7 type NB set GC.1.C8 type CK set GC.1.H8 type "H5" set GC.1.N9 type "N*" set GC.1.C4 type CB set GC.1.N3 type NC set GC.1.C2 type CA set GC.1.N1 type NA set GC.1.H1 type H set G5 name "G5" set G5 head G5.1.C5' # tail null set G5.1 connect0 G5.1.C5' set G5.1 connect1 G5.1.C2' set G5.1 restype nucleic set G5.1 name "G5" # set FF atom types set G5.1.O3' type OH set G5.1.H3T type HO set G5.1.C5' type CT set G5.1.H5'1 type H1 set G5.1.H5'2 type H1 set G5.1.O4' type OS set G5.1.C4' type CT set G5.1.H4' type H1 set G5.1.C3' type CT set G5.1.H3' type H1 set G5.1.C2' type CT set G5.1.H2'1 type "HC" set G5.1.H2'2 type "HC" set G5.1.C1' type CT set G5.1.H1' type "H2" set G5.1.N2 type N2 set G5.1.H21 type H set G5.1.H22 type H set G5.1.O6 type O set G5.1.C6 type C set G5.1.C5 type CB set G5.1.N7 type NB set G5.1.C8 type CK set G5.1.H8 type "H5" set G5.1.N9 type "N*" set G5.1.C4 type CB set G5.1.N3 type NC set G5.1.C2 type CA set G5.1.N1 type NA set G5.1.H1 type H set G3 name "G3" set G3 head G3.1.C3' # tail null set G3.1 connect0 G3.1.C3' set G3.1 connect1 G3.1.C2' set G3.1 restype nucleic set G3.1 name "G3" # set FF atom types set G3.1.O5' type OH set G3.1.H5T type HO set G3.1.C5' type CT set G3.1.H5'1 type H1 set G3.1.H5'2 type H1 set G3.1.O4' type OS set G3.1.C4' type CT set G3.1.H4' type H1 set G3.1.C3' type CT set G3.1.H3' type H1 set G3.1.C2' type CT set G3.1.H2'1 type "HC" set G3.1.H2'2 type "HC" set G3.1.C1' type CT set G3.1.H1' type "H2" set G3.1.N2 type N2 set G3.1.H21 type H set G3.1.H22 type H set G3.1.O6 type O set G3.1.C6 type C set G3.1.C5 type CB set G3.1.N7 type NB set G3.1.C8 type CK set G3.1.H8 type "H5" set G3.1.N9 type "N*" set G3.1.C4 type CB set G3.1.N3 type NC set G3.1.C2 type CA set G3.1.N1 type NA set G3.1.H1 type H # ------- 2-deoxy-thymidine nucleoside fragments ----------- set TN name "TN" # head & tail null set TN.1 connect0 TN.1.C5' set TN.1 connect1 TN.1.C2' set TN.1 restype nucleic set TN.1 name "TN" # set FF atom types set TN.1.O5' type OH set TN.1.H5T type HO set TN.1.O3' type OH set TN.1.H3T type HO set TN.1.C5' type CT set TN.1.H5'1 type H1 set TN.1.H5'2 type H1 set TN.1.O4' type OS set TN.1.C4' type CT set TN.1.H4' type H1 set TN.1.C3' type CT set TN.1.H3' type H1 set TN.1.C2' type CT set TN.1.H2'1 type "HC" set TN.1.H2'2 type "HC" set TN.1.C1' type CT set TN.1.H1' type "H2" set TN.1.O4 type O set TN.1.C4 type C set TN.1.N3 type NA set TN.1.H3 type H set TN.1.C2 type C set TN.1.O2 type O set TN.1.N1 type "N*" set TN.1.C6 type CM set TN.1.H6 type H4 set TN.1.C5 type CM set TN.1.C7 type CT set TN.1.H71 type "HC" set TN.1.H72 type "HC" set TN.1.H73 type "HC" set TC name "TC" set TC head TC.1.C5' set TC tail TC.1.C2' set TC.1 connect0 TC.1.C5' set TC.1 connect1 TC.1.C2' set TC.1 restype nucleic set TC.1 name "TC" # set FF atom types set TC.1.C5' type CT set TC.1.H5'1 type H1 set TC.1.H5'2 type H1 set TC.1.O4' type OS set TC.1.C4' type CT set TC.1.H4' type H1 set TC.1.C3' type CT set TC.1.H3' type H1 set TC.1.C2' type CT set TC.1.H2'1 type "HC" set TC.1.H2'2 type "HC" set TC.1.C1' type CT set TC.1.H1' type "H2" set TC.1.O4 type O set TC.1.C4 type C set TC.1.N3 type NA set TC.1.H3 type H set TC.1.C2 type C set TC.1.O2 type O set TC.1.N1 type "N*" set TC.1.C6 type CM set TC.1.H6 type H4 set TC.1.C5 type CM set TC.1.C7 type CT set TC.1.H71 type "HC" set TC.1.H72 type "HC" set TC.1.H73 type "HC" set T5 name "T5" set T5 head T5.1.C5' # tail null set T5.1 connect0 T5.1.C5' set T5.1 connect1 T5.1.C2' set T5.1 restype nucleic set T5.1 name "T5" # set FF atom types set T5.1.O3' type OH set T5.1.H3T type HO set T5.1.C5' type CT set T5.1.H5'1 type H1 set T5.1.H5'2 type H1 set T5.1.O4' type OS set T5.1.C4' type CT set T5.1.H4' type H1 set T5.1.C3' type CT set T5.1.H3' type H1 set T5.1.C2' type CT set T5.1.H2'1 type "HC" set T5.1.H2'2 type "HC" set T5.1.C1' type CT set T5.1.H1' type "H2" set T5.1.O4 type O set T5.1.C4 type C set T5.1.N3 type NA set T5.1.H3 type H set T5.1.C2 type C set T5.1.O2 type O set T5.1.N1 type "N*" set T5.1.C6 type CM set T5.1.H6 type H4 set T5.1.C5 type CM set T5.1.C7 type CT set T5.1.H71 type "HC" set T5.1.H72 type "HC" set T5.1.H73 type "HC" set T3 name "T3" set T3 head T3.1.C3' # tail null set T3.1 connect0 T3.1.C3' set T3.1 connect1 T3.1.C2' set T3.1 restype nucleic set T3.1 name "T3" # set FF atom types set T3.1.O5' type OH set T3.1.H5T type HO set T3.1.C5' type CT set T3.1.H5'1 type H1 set T3.1.H5'2 type H1 set T3.1.O4' type OS set T3.1.C4' type CT set T3.1.H4' type H1 set T3.1.C3' type CT set T3.1.H3' type H1 set T3.1.C2' type CT set T3.1.H2'1 type "HC" set T3.1.H2'2 type "HC" set T3.1.C1' type CT set T3.1.H1' type "H2" set T3.1.O4 type O set T3.1.C4 type C set T3.1.N3 type NA set T3.1.H3 type H set T3.1.C2 type C set T3.1.O2 type O set T3.1.N1 type "N*" set T3.1.C6 type CM set T3.1.H6 type H4 set T3.1.C5 type CM set T3.1.C7 type CT set T3.1.H71 type "HC" set T3.1.H72 type "HC" set T3.1.H73 type "HC" # ------- Adenosine nucleoside fragments ----------- set BN name "BN" # head & tail null set BN.1 connect0 BN.1.C5' set BN.1 connect1 BN.1.C2' set BN.1 restype nucleic set BN.1 name "BN" # set FF atom types set BN.1.O5' type OH set BN.1.H5T type HO set BN.1.O3' type OH set BN.1.H3T type HO set BN.1.C5' type CT set BN.1.H5'1 type H1 set BN.1.H5'2 type H1 set BN.1.O4' type OS set BN.1.C4' type CT set BN.1.H4' type H1 set BN.1.C3' type CT set BN.1.H3' type H1 set BN.1.C2' type CT set BN.1.H2' type H1 set BN.1.O2' type OH set BN.1.H2T type HO set BN.1.C1' type CT set BN.1.H1' type "H2" set BN.1.N6 type N2 set BN.1.H61 type H set BN.1.H62 type H set BN.1.C6 type CA set BN.1.C5 type CB set BN.1.N7 type NB set BN.1.C8 type CK set BN.1.H8 type "H5" set BN.1.N9 type "N*" set BN.1.C4 type CB set BN.1.N3 type NC set BN.1.C2 type CQ set BN.1.H2 type "H5" set BN.1.N1 type NC set BC name "BC" set BC head BC.1.C5' set BC tail BC.1.C2' set BC.1 connect0 BC.1.C5' set BC.1 connect1 BC.1.C2' set BC.1 restype nucleic set BC.1 name "BC" # set FF atom types set BC.1.C5' type CT set BC.1.H5'1 type H1 set BC.1.H5'2 type H1 set BC.1.O4' type OS set BC.1.C4' type CT set BC.1.H4' type H1 set BC.1.C3' type CT set BC.1.H3' type H1 set BC.1.C2' type CT set BC.1.H2' type H1 set BC.1.C1' type CT set BC.1.H1' type "H2" set BC.1.N6 type N2 set BC.1.H61 type H set BC.1.H62 type H set BC.1.C6 type CA set BC.1.C5 type CB set BC.1.N7 type NB set BC.1.C8 type CK set BC.1.H8 type "H5" set BC.1.N9 type "N*" set BC.1.C4 type CB set BC.1.N3 type NC set BC.1.C2 type CQ set BC.1.H2 type "H5" set BC.1.N1 type NC set B5 name "B5" set B5 head B5.1.C5' # tail null set B5.1 connect0 B5.1.C5' set B5.1 connect1 B5.1.C2' set B5.1 restype nucleic set B5.1 name "B5" # set FF atom types set B5.1.O3' type OH set B5.1.H3T type HO set B5.1.C5' type CT set B5.1.H5'1 type H1 set B5.1.H5'2 type H1 set B5.1.O4' type OS set B5.1.C4' type CT set B5.1.H4' type H1 set B5.1.C3' type CT set B5.1.H3' type H1 set B5.1.C2' type CT set B5.1.H2' type H1 set B5.1.O2' type OH set B5.1.H2T type HO set B5.1.C1' type CT set B5.1.H1' type "H2" set B5.1.N6 type N2 set B5.1.H61 type H set B5.1.H62 type H set B5.1.C6 type CA set B5.1.C5 type CB set B5.1.N7 type NB set B5.1.C8 type CK set B5.1.H8 type "H5" set B5.1.N9 type "N*" set B5.1.C4 type CB set B5.1.N3 type NC set B5.1.C2 type CQ set B5.1.H2 type "H5" set B5.1.N1 type NC set B3 name "B3" set B3 head B3.1.C3' # tail null set B3.1 connect0 B3.1.C3' set B3.1 connect1 B3.1.C2' set B3.1 restype nucleic set B3.1 name "B3" # set FF atom types set B3.1.O5' type OH set B3.1.H5T type HO set B3.1.C5' type CT set B3.1.H5'1 type H1 set B3.1.H5'2 type H1 set B3.1.O4' type OS set B3.1.C4' type CT set B3.1.H4' type H1 set B3.1.C3' type CT set B3.1.H3' type H1 set B3.1.C2' type CT set B3.1.H2' type H1 set B3.1.O2' type OH set B3.1.H2T type HO set B3.1.C1' type CT set B3.1.H1' type "H2" set B3.1.N6 type N2 set B3.1.H61 type H set B3.1.H62 type H set B3.1.C6 type CA set B3.1.C5 type CB set B3.1.N7 type NB set B3.1.C8 type CK set B3.1.H8 type "H5" set B3.1.N9 type "N*" set B3.1.C4 type CB set B3.1.N3 type NC set B3.1.C2 type CQ set B3.1.H2 type "H5" set B3.1.N1 type NC set B2 name "B2" set B2 head B2.1.C2' # tail null set B2.1 connect0 B2.1.C2' set B2.1 connect1 B2.1.C3' set B2.1 restype nucleic set B2.1 name "B2" # set FF atom types set B2.1.O5' type OH set B2.1.H5T type HO set B2.1.O3' type OH set B2.1.H3T type HO set B2.1.C5' type CT set B2.1.H5'1 type H1 set B2.1.H5'2 type H1 set B2.1.O4' type OS set B2.1.C4' type CT set B2.1.H4' type H1 set B2.1.C3' type CT set B2.1.H3' type H1 set B2.1.C2' type CT set B2.1.H2' type H1 set B2.1.C1' type CT set B2.1.H1' type "H2" set B2.1.N6 type N2 set B2.1.H61 type H set B2.1.H62 type H set B2.1.C6 type CA set B2.1.C5 type CB set B2.1.N7 type NB set B2.1.C8 type CK set B2.1.H8 type "H5" set B2.1.N9 type "N*" set B2.1.C4 type CB set B2.1.N3 type NC set B2.1.C2 type CQ set B2.1.H2 type "H5" set B2.1.N1 type NC set B53 name "B53" set B53 head B53.1.C5' set B53 tail B53.1.C3' set B53.1 connect0 B53.1.C5' set B53.1 connect1 B53.1.C3' set B53.1 restype nucleic set B53.1 name "B53" # set FF atom types set B53.1.C5' type CT set B53.1.H5'1 type H1 set B53.1.H5'2 type H1 set B53.1.O4' type OS set B53.1.C4' type CT set B53.1.H4' type H1 set B53.1.C3' type CT set B53.1.H3' type H1 set B53.1.C2' type CT set B53.1.H2' type H1 set B53.1.O2' type OH set B53.1.H2T type HO set B53.1.C1' type CT set B53.1.H1' type "H2" set B53.1.N6 type N2 set B53.1.H61 type H set B53.1.H62 type H set B53.1.C6 type CA set B53.1.C5 type CB set B53.1.N7 type NB set B53.1.C8 type CK set B53.1.H8 type "H5" set B53.1.N9 type "N*" set B53.1.C4 type CB set B53.1.N3 type NC set B53.1.C2 type CQ set B53.1.H2 type "H5" set B53.1.N1 type NC set B52 name "B52" set B52 head B52.1.C5' set B52 tail B52.1.C2' set B52.1 connect0 B52.1.C5' set B52.1 connect1 B52.1.C2' set B52.1 restype nucleic set B52.1 name "B52" # set FF atom types set B52.1.O3' type OH set B52.1.H3T type HO set B52.1.C5' type CT set B52.1.H5'1 type H1 set B52.1.H5'2 type H1 set B52.1.O4' type OS set B52.1.C4' type CT set B52.1.H4' type H1 set B52.1.C3' type CT set B52.1.H3' type H1 set B52.1.C2' type CT set B52.1.H2' type H1 set B52.1.C1' type CT set B52.1.H1' type "H2" set B52.1.N6 type N2 set B52.1.H61 type H set B52.1.H62 type H set B52.1.C6 type CA set B52.1.C5 type CB set B52.1.N7 type NB set B52.1.C8 type CK set B52.1.H8 type "H5" set B52.1.N9 type "N*" set B52.1.C4 type CB set B52.1.N3 type NC set B52.1.C2 type CQ set B52.1.H2 type "H5" set B52.1.N1 type NC set B32 name "B32" set B32 head B32.1.C3' set B32 tail B32.1.C2' set B32.1 connect0 B32.1.C3' set B32.1 connect1 B32.1.C2' set B32.1 restype nucleic set B32.1 name "B32" # set FF atom types set B32.1.O5' type OH set B32.1.H5T type HO set B32.1.C5' type CT set B32.1.H5'1 type H1 set B32.1.H5'2 type H1 set B32.1.O4' type OS set B32.1.C4' type CT set B32.1.H4' type H1 set B32.1.C3' type CT set B32.1.H3' type H1 set B32.1.C2' type CT set B32.1.H2' type H1 set B32.1.C1' type CT set B32.1.H1' type "H2" set B32.1.N6 type N2 set B32.1.H61 type H set B32.1.H62 type H set B32.1.C6 type CA set B32.1.C5 type CB set B32.1.N7 type NB set B32.1.C8 type CK set B32.1.H8 type "H5" set B32.1.N9 type "N*" set B32.1.C4 type CB set B32.1.N3 type NC set B32.1.C2 type CQ set B32.1.H2 type "H5" set B32.1.N1 type NC # ------- Cystosine nucleoside fragments ----------- set DN name "DN" # head & tail null set DN.1 connect0 DN.1.C5' set DN.1 connect1 DN.1.C2' set DN.1 restype nucleic set DN.1 name "DN" # set FF atom types set DN.1.O5' type OH set DN.1.H5T type HO set DN.1.O3' type OH set DN.1.H3T type HO set DN.1.C5' type CT set DN.1.H5'1 type H1 set DN.1.H5'2 type H1 set DN.1.O4' type OS set DN.1.C4' type CT set DN.1.H4' type H1 set DN.1.C3' type CT set DN.1.H3' type H1 set DN.1.C2' type CT set DN.1.H2' type H1 set DN.1.O2' type OH set DN.1.H2T type HO set DN.1.C1' type CT set DN.1.H1' type "H2" set DN.1.N4 type N2 set DN.1.H41 type H set DN.1.H42 type H set DN.1.C4 type CA set DN.1.N3 type NC set DN.1.C2 type C set DN.1.O2 type O set DN.1.N1 type "N*" set DN.1.C6 type CM set DN.1.H6 type H4 set DN.1.C5 type CM set DN.1.H5 type HA set DC name "DC" set DC head DC.1.C5' set DC tail DC.1.C2' set DC.1 connect0 DC.1.C5' set DC.1 connect1 DC.1.C2' set DC.1 restype nucleic set DC.1 name "DC" # set FF atom types set DC.1.C5' type CT set DC.1.H5'1 type H1 set DC.1.H5'2 type H1 set DC.1.O4' type OS set DC.1.C4' type CT set DC.1.H4' type H1 set DC.1.C3' type CT set DC.1.H3' type H1 set DC.1.C2' type CT set DC.1.H2' type H1 set DC.1.C1' type CT set DC.1.H1' type "H2" set DC.1.N4 type N2 set DC.1.H41 type H set DC.1.H42 type H set DC.1.C4 type CA set DC.1.N3 type NC set DC.1.C2 type C set DC.1.O2 type O set DC.1.N1 type "N*" set DC.1.C6 type CM set DC.1.H6 type H4 set DC.1.C5 type CM set DC.1.H5 type HA set D5 name "D5" set D5 head D5.1.C5' # tail null set D5.1 connect0 D5.1.C5' set D5.1 connect1 D5.1.C2' set D5.1 restype nucleic set D5.1 name "D5" # set FF atom types set D5.1.O3' type OH set D5.1.H3T type HO set D5.1.C5' type CT set D5.1.H5'1 type H1 set D5.1.H5'2 type H1 set D5.1.O4' type OS set D5.1.C4' type CT set D5.1.H4' type H1 set D5.1.C3' type CT set D5.1.H3' type H1 set D5.1.C2' type CT set D5.1.H2' type H1 set D5.1.O2' type OH set D5.1.H2T type HO set D5.1.C1' type CT set D5.1.H1' type "H2" set D5.1.N4 type N2 set D5.1.H41 type H set D5.1.H42 type H set D5.1.C4 type CA set D5.1.N3 type NC set D5.1.C2 type C set D5.1.O2 type O set D5.1.N1 type "N*" set D5.1.C6 type CM set D5.1.H6 type H4 set D5.1.C5 type CM set D5.1.H5 type HA set D3 name "D3" set D3 head D3.1.C3' # tail null set D3.1 connect0 D3.1.C3' set D3.1 connect1 D3.1.C2' set D3.1 restype nucleic set D3.1 name "D3" # set FF atom types set D3.1.O5' type OH set D3.1.H5T type HO set D3.1.C5' type CT set D3.1.H5'1 type H1 set D3.1.H5'2 type H1 set D3.1.O4' type OS set D3.1.C4' type CT set D3.1.H4' type H1 set D3.1.C3' type CT set D3.1.H3' type H1 set D3.1.C2' type CT set D3.1.H2' type H1 set D3.1.O2' type OH set D3.1.H2T type HO set D3.1.C1' type CT set D3.1.H1' type "H2" set D3.1.N4 type N2 set D3.1.H41 type H set D3.1.H42 type H set D3.1.C4 type CA set D3.1.N3 type NC set D3.1.C2 type C set D3.1.O2 type O set D3.1.N1 type "N*" set D3.1.C6 type CM set D3.1.H6 type H4 set D3.1.C5 type CM set D3.1.H5 type HA set D2 name "D2" set D2 head D2.1.C2' # tail null set D2.1 connect0 D2.1.C2' set D2.1 connect1 D2.1.C3' set D2.1 restype nucleic set D2.1 name "D2" # set FF atom types set D2.1.O5' type OH set D2.1.H5T type HO set D2.1.O3' type OH set D2.1.H3T type HO set D2.1.C5' type CT set D2.1.H5'1 type H1 set D2.1.H5'2 type H1 set D2.1.O4' type OS set D2.1.C4' type CT set D2.1.H4' type H1 set D2.1.C3' type CT set D2.1.H3' type H1 set D2.1.C2' type CT set D2.1.H2' type H1 set D2.1.C1' type CT set D2.1.H1' type "H2" set D2.1.N4 type N2 set D2.1.H41 type H set D2.1.H42 type H set D2.1.C4 type CA set D2.1.N3 type NC set D2.1.C2 type C set D2.1.O2 type O set D2.1.N1 type "N*" set D2.1.C6 type CM set D2.1.H6 type H4 set D2.1.C5 type CM set D2.1.H5 type HA set D53 name "D53" set D53 head D53.1.C5' set D53 tail D53.1.C3' set D53.1 connect0 D53.1.C5' set D53.1 connect1 D53.1.C3' set D53.1 restype nucleic set D53.1 name "D53" # set FF atom types set D53.1.C5' type CT set D53.1.H5'1 type H1 set D53.1.H5'2 type H1 set D53.1.O4' type OS set D53.1.C4' type CT set D53.1.H4' type H1 set D53.1.C3' type CT set D53.1.H3' type H1 set D53.1.C2' type CT set D53.1.H2' type H1 set D53.1.O2' type OH set D53.1.H2T type HO set D53.1.C1' type CT set D53.1.H1' type "H2" set D53.1.N4 type N2 set D53.1.H41 type H set D53.1.H42 type H set D53.1.C4 type CA set D53.1.N3 type NC set D53.1.C2 type C set D53.1.O2 type O set D53.1.N1 type "N*" set D53.1.C6 type CM set D53.1.H6 type H4 set D53.1.C5 type CM set D53.1.H5 type HA set D52 name "D52" set D52 head D52.1.C5' set D52 tail D52.1.C2' set D52.1 connect0 D52.1.C5' set D52.1 connect1 D52.1.C2' set D52.1 restype nucleic set D52.1 name "D52" # set FF atom types set D52.1.O3' type OH set D52.1.H3T type HO set D52.1.C5' type CT set D52.1.H5'1 type H1 set D52.1.H5'2 type H1 set D52.1.O4' type OS set D52.1.C4' type CT set D52.1.H4' type H1 set D52.1.C3' type CT set D52.1.H3' type H1 set D52.1.C2' type CT set D52.1.H2' type H1 set D52.1.C1' type CT set D52.1.H1' type "H2" set D52.1.N4 type N2 set D52.1.H41 type H set D52.1.H42 type H set D52.1.C4 type CA set D52.1.N3 type NC set D52.1.C2 type C set D52.1.O2 type O set D52.1.N1 type "N*" set D52.1.C6 type CM set D52.1.H6 type H4 set D52.1.C5 type CM set D52.1.H5 type HA set D32 name "D32" set D32 head D32.1.C3' set D32 tail D32.1.C2' set D32.1 connect0 D32.1.C3' set D32.1 connect1 D32.1.C2' set D32.1 restype nucleic set D32.1 name "D32" # set FF atom types set D32.1.O5' type OH set D32.1.H5T type HO set D32.1.C5' type CT set D32.1.H5'1 type H1 set D32.1.H5'2 type H1 set D32.1.O4' type OS set D32.1.C4' type CT set D32.1.H4' type H1 set D32.1.C3' type CT set D32.1.H3' type H1 set D32.1.C2' type CT set D32.1.H2' type H1 set D32.1.C1' type CT set D32.1.H1' type "H2" set D32.1.N4 type N2 set D32.1.H41 type H set D32.1.H42 type H set D32.1.C4 type CA set D32.1.N3 type NC set D32.1.C2 type C set D32.1.O2 type O set D32.1.N1 type "N*" set D32.1.C6 type CM set D32.1.H6 type H4 set D32.1.C5 type CM set D32.1.H5 type HA # ------- Guanosine nucleoside fragments ----------- set HN name "HN" # head & tail null set HN.1 connect0 HN.1.C5' set HN.1 connect1 HN.1.C2' set HN.1 restype nucleic set HN.1 name "HN" # set FF atom types set HN.1.O5' type OH set HN.1.H5T type HO set HN.1.O3' type OH set HN.1.H3T type HO set HN.1.C5' type CT set HN.1.H5'1 type H1 set HN.1.H5'2 type H1 set HN.1.O4' type OS set HN.1.C4' type CT set HN.1.H4' type H1 set HN.1.C3' type CT set HN.1.H3' type H1 set HN.1.C2' type CT set HN.1.H2' type H1 set HN.1.O2' type OH set HN.1.H2T type HO set HN.1.C1' type CT set HN.1.H1' type "H2" set HN.1.N2 type N2 set HN.1.H21 type H set HN.1.H22 type H set HN.1.O6 type O set HN.1.C6 type C set HN.1.C5 type CB set HN.1.N7 type NB set HN.1.C8 type CK set HN.1.H8 type "H5" set HN.1.N9 type "N*" set HN.1.C4 type CB set HN.1.N3 type NC set HN.1.C2 type CA set HN.1.N1 type NA set HN.1.H1 type H set HC name "HC" set HC head HC.1.C5' set HC tail HC.1.C2' set HC.1 connect0 HC.1.C5' set HC.1 connect1 HC.1.C2' set HC.1 restype nucleic set HC.1 name "HC" # set FF atom types set HC.1.C5' type CT set HC.1.H5'1 type H1 set HC.1.H5'2 type H1 set HC.1.O4' type OS set HC.1.C4' type CT set HC.1.H4' type H1 set HC.1.C3' type CT set HC.1.H3' type H1 set HC.1.C2' type CT set HC.1.H2' type H1 set HC.1.C1' type CT set HC.1.H1' type "H2" set HC.1.N2 type N2 set HC.1.H21 type H set HC.1.H22 type H set HC.1.O6 type O set HC.1.C6 type C set HC.1.C5 type CB set HC.1.N7 type NB set HC.1.C8 type CK set HC.1.H8 type "H5" set HC.1.N9 type "N*" set HC.1.C4 type CB set HC.1.N3 type NC set HC.1.C2 type CA set HC.1.N1 type NA set HC.1.H1 type H set H5 name "H5" set H5 head H5.1.C5' # tail null set H5.1 connect0 H5.1.C5' set H5.1 connect1 H5.1.C2' set H5.1 restype nucleic set H5.1 name "H5" # set FF atom types set H5.1.O3' type OH set H5.1.H3T type HO set H5.1.C5' type CT set H5.1.H5'1 type H1 set H5.1.H5'2 type H1 set H5.1.O4' type OS set H5.1.C4' type CT set H5.1.H4' type H1 set H5.1.C3' type CT set H5.1.H3' type H1 set H5.1.C2' type CT set H5.1.H2' type H1 set H5.1.O2' type OH set H5.1.H2T type HO set H5.1.C1' type CT set H5.1.H1' type "H2" set H5.1.N2 type N2 set H5.1.H21 type H set H5.1.H22 type H set H5.1.O6 type O set H5.1.C6 type C set H5.1.C5 type CB set H5.1.N7 type NB set H5.1.C8 type CK set H5.1.H8 type "H5" set H5.1.N9 type "N*" set H5.1.C4 type CB set H5.1.N3 type NC set H5.1.C2 type CA set H5.1.N1 type NA set H5.1.H1 type H set H3 name "H3" set H3 head H3.1.C3' # tail null set H3.1 connect0 H3.1.C3' set H3.1 connect1 H3.1.C2' set H3.1 restype nucleic set H3.1 name "H3" # set FF atom types set H3.1.O5' type OH set H3.1.H5T type HO set H3.1.C5' type CT set H3.1.H5'1 type H1 set H3.1.H5'2 type H1 set H3.1.O4' type OS set H3.1.C4' type CT set H3.1.H4' type H1 set H3.1.C3' type CT set H3.1.H3' type H1 set H3.1.C2' type CT set H3.1.H2' type H1 set H3.1.O2' type OH set H3.1.H2T type HO set H3.1.C1' type CT set H3.1.H1' type "H2" set H3.1.N2 type N2 set H3.1.H21 type H set H3.1.H22 type H set H3.1.O6 type O set H3.1.C6 type C set H3.1.C5 type CB set H3.1.N7 type NB set H3.1.C8 type CK set H3.1.H8 type "H5" set H3.1.N9 type "N*" set H3.1.C4 type CB set H3.1.N3 type NC set H3.1.C2 type CA set H3.1.N1 type NA set H3.1.H1 type H set H2 name "H2" set H2 head H2.1.C2' # tail null set H2.1 connect0 H2.1.C2' set H2.1 connect1 H2.1.C3' set H2.1 restype nucleic set H2.1 name "H2" # set FF atom types set H2.1.O5' type OH set H2.1.H5T type HO set H2.1.O3' type OH set H2.1.H3T type HO set H2.1.C5' type CT set H2.1.H5'1 type H1 set H2.1.H5'2 type H1 set H2.1.O4' type OS set H2.1.C4' type CT set H2.1.H4' type H1 set H2.1.C3' type CT set H2.1.H3' type H1 set H2.1.C2' type CT set H2.1.H2' type H1 set H2.1.C1' type CT set H2.1.H1' type "H2" set H2.1.N2 type N2 set H2.1.H21 type H set H2.1.H22 type H set H2.1.O6 type O set H2.1.C6 type C set H2.1.C5 type CB set H2.1.N7 type NB set H2.1.C8 type CK set H2.1.H8 type "H5" set H2.1.N9 type "N*" set H2.1.C4 type CB set H2.1.N3 type NC set H2.1.C2 type CA set H2.1.N1 type NA set H2.1.H1 type H set H53 name "H53" set H53 head H53.1.C5' set H53 tail H53.1.C3' set H53.1 connect0 H53.1.C5' set H53.1 connect1 H53.1.C3' set H53.1 restype nucleic set H53.1 name "H53" # set FF atom types set H53.1.C5' type CT set H53.1.H5'1 type H1 set H53.1.H5'2 type H1 set H53.1.O4' type OS set H53.1.C4' type CT set H53.1.H4' type H1 set H53.1.C3' type CT set H53.1.H3' type H1 set H53.1.C2' type CT set H53.1.H2' type H1 set H53.1.O2' type OH set H53.1.H2T type HO set H53.1.C1' type CT set H53.1.H1' type "H2" set H53.1.N2 type N2 set H53.1.H21 type H set H53.1.H22 type H set H53.1.O6 type O set H53.1.C6 type C set H53.1.C5 type CB set H53.1.N7 type NB set H53.1.C8 type CK set H53.1.H8 type "H5" set H53.1.N9 type "N*" set H53.1.C4 type CB set H53.1.N3 type NC set H53.1.C2 type CA set H53.1.N1 type NA set H53.1.H1 type H set H52 name "H52" set H52 head H52.1.C5' set H52 tail H52.1.C2' set H52.1 connect0 H52.1.C5' set H52.1 connect1 H52.1.C2' set H52.1 restype nucleic set H52.1 name "H52" # set FF atom types set H52.1.O3' type OH set H52.1.H3T type HO set H52.1.C5' type CT set H52.1.H5'1 type H1 set H52.1.H5'2 type H1 set H52.1.O4' type OS set H52.1.C4' type CT set H52.1.H4' type H1 set H52.1.C3' type CT set H52.1.H3' type H1 set H52.1.C2' type CT set H52.1.H2' type H1 set H52.1.C1' type CT set H52.1.H1' type "H2" set H52.1.N2 type N2 set H52.1.H21 type H set H52.1.H22 type H set H52.1.O6 type O set H52.1.C6 type C set H52.1.C5 type CB set H52.1.N7 type NB set H52.1.C8 type CK set H52.1.H8 type "H5" set H52.1.N9 type "N*" set H52.1.C4 type CB set H52.1.N3 type NC set H52.1.C2 type CA set H52.1.N1 type NA set H52.1.H1 type H set H32 name "H32" set H32 head H32.1.C3' set H32 tail H32.1.C2' set H32.1 connect0 H32.1.C3' set H32.1 connect1 H32.1.C2' set H32.1 restype nucleic set H32.1 name "H32" # set FF atom types set H32.1.O5' type OH set H32.1.H5T type HO set H32.1.C5' type CT set H32.1.H5'1 type H1 set H32.1.H5'2 type H1 set H32.1.O4' type OS set H32.1.C4' type CT set H32.1.H4' type H1 set H32.1.C3' type CT set H32.1.H3' type H1 set H32.1.C2' type CT set H32.1.H2' type H1 set H32.1.C1' type CT set H32.1.H1' type "H2" set H32.1.N2 type N2 set H32.1.H21 type H set H32.1.H22 type H set H32.1.O6 type O set H32.1.C6 type C set H32.1.C5 type CB set H32.1.N7 type NB set H32.1.C8 type CK set H32.1.H8 type "H5" set H32.1.N9 type "N*" set H32.1.C4 type CB set H32.1.N3 type NC set H32.1.C2 type CA set H32.1.N1 type NA set H32.1.H1 type H # ------- Uridine nucleoside fragments ----------- set UN name "UN" # head & tail null set UN.1 connect0 UN.1.C5' set UN.1 connect1 UN.1.C2' set UN.1 restype nucleic set UN.1 name "UN" # set FF atom types set UN.1.O5' type OH set UN.1.H5T type HO set UN.1.O3' type OH set UN.1.H3T type HO set UN.1.C5' type CT set UN.1.H5'1 type H1 set UN.1.H5'2 type H1 set UN.1.O4' type OS set UN.1.C4' type CT set UN.1.H4' type H1 set UN.1.C3' type CT set UN.1.H3' type H1 set UN.1.C2' type CT set UN.1.H2' type H1 set UN.1.O2' type OH set UN.1.H2T type HO set UN.1.C1' type CT set UN.1.H1' type "H2" set UN.1.O4 type O set UN.1.C4 type C set UN.1.N3 type NA set UN.1.H3 type H set UN.1.C2 type C set UN.1.O2 type O set UN.1.N1 type "N*" set UN.1.C6 type CM set UN.1.H6 type H4 set UN.1.C5 type CM set UN.1.H5 type HA set UC name "UC" set UC head UC.1.C5' set UC tail UC.1.C2' set UC.1 connect0 UC.1.C5' set UC.1 connect1 UC.1.C2' set UC.1 restype nucleic set UC.1 name "UC" # set FF atom types set UC.1.C5' type CT set UC.1.H5'1 type H1 set UC.1.H5'2 type H1 set UC.1.O4' type OS set UC.1.C4' type CT set UC.1.H4' type H1 set UC.1.C3' type CT set UC.1.H3' type H1 set UC.1.C2' type CT set UC.1.H2' type H1 set UC.1.C1' type CT set UC.1.H1' type "H2" set UC.1.O4 type O set UC.1.C4 type C set UC.1.N3 type NA set UC.1.H3 type H set UC.1.C2 type C set UC.1.O2 type O set UC.1.N1 type "N*" set UC.1.C6 type CM set UC.1.H6 type H4 set UC.1.C5 type CM set UC.1.H5 type HA set U5 name "U5" set U5 head U5.1.C5' # tail null set U5.1 connect0 U5.1.C5' set U5.1 connect1 U5.1.C2' set U5.1 restype nucleic set U5.1 name "U5" # set FF atom types set U5.1.O3' type OH set U5.1.H3T type HO set U5.1.C5' type CT set U5.1.H5'1 type H1 set U5.1.H5'2 type H1 set U5.1.O4' type OS set U5.1.C4' type CT set U5.1.H4' type H1 set U5.1.C3' type CT set U5.1.H3' type H1 set U5.1.C2' type CT set U5.1.H2' type H1 set U5.1.O2' type OH set U5.1.H2T type HO set U5.1.C1' type CT set U5.1.H1' type "H2" set U5.1.O4 type O set U5.1.C4 type C set U5.1.N3 type NA set U5.1.H3 type H set U5.1.C2 type C set U5.1.O2 type O set U5.1.N1 type "N*" set U5.1.C6 type CM set U5.1.H6 type H4 set U5.1.C5 type CM set U5.1.H5 type HA set U3 name "U3" set U3 head U3.1.C3' # tail null set U3.1 connect0 U3.1.C3' set U3.1 connect1 U3.1.C2' set U3.1 restype nucleic set U3.1 name "U3" # set FF atom types set U3.1.O5' type OH set U3.1.H5T type HO set U3.1.C5' type CT set U3.1.H5'1 type H1 set U3.1.H5'2 type H1 set U3.1.O4' type OS set U3.1.C4' type CT set U3.1.H4' type H1 set U3.1.C3' type CT set U3.1.H3' type H1 set U3.1.C2' type CT set U3.1.H2' type H1 set U3.1.O2' type OH set U3.1.H2T type HO set U3.1.C1' type CT set U3.1.H1' type "H2" set U3.1.O4 type O set U3.1.C4 type C set U3.1.N3 type NA set U3.1.H3 type H set U3.1.C2 type C set U3.1.O2 type O set U3.1.N1 type "N*" set U3.1.C6 type CM set U3.1.H6 type H4 set U3.1.C5 type CM set U3.1.H5 type HA set U2 name "U2" set U2 head U2.1.C2' # tail null set U2.1 connect0 U2.1.C2' set U2.1 connect1 U2.1.C3' set U2.1 restype nucleic set U2.1 name "U2" # set FF atom types set U2.1.O5' type OH set U2.1.H5T type HO set U2.1.O3' type OH set U2.1.H3T type HO set U2.1.C5' type CT set U2.1.H5'1 type H1 set U2.1.H5'2 type H1 set U2.1.O4' type OS set U2.1.C4' type CT set U2.1.H4' type H1 set U2.1.C3' type CT set U2.1.H3' type H1 set U2.1.C2' type CT set U2.1.H2' type H1 set U2.1.C1' type CT set U2.1.H1' type "H2" set U2.1.O4 type O set U2.1.C4 type C set U2.1.N3 type NA set U2.1.H3 type H set U2.1.C2 type C set U2.1.O2 type O set U2.1.N1 type "N*" set U2.1.C6 type CM set U2.1.H6 type H4 set U2.1.C5 type CM set U2.1.H5 type HA set U53 name "U53" set U53 head U53.1.C5' set U53 tail U53.1.C3' set U53.1 connect0 U53.1.C5' set U53.1 connect1 U53.1.C3' set U53.1 restype nucleic set U53.1 name "U53" # set FF atom types set U53.1.C5' type CT set U53.1.H5'1 type H1 set U53.1.H5'2 type H1 set U53.1.O4' type OS set U53.1.C4' type CT set U53.1.H4' type H1 set U53.1.C3' type CT set U53.1.H3' type H1 set U53.1.C2' type CT set U53.1.H2' type H1 set U53.1.O2' type OH set U53.1.H2T type HO set U53.1.C1' type CT set U53.1.H1' type "H2" set U53.1.O4 type O set U53.1.C4 type C set U53.1.N3 type NA set U53.1.H3 type H set U53.1.C2 type C set U53.1.O2 type O set U53.1.N1 type "N*" set U53.1.C6 type CM set U53.1.H6 type H4 set U53.1.C5 type CM set U53.1.H5 type HA set U52 name "U52" set U52 head U52.1.C5' set U52 tail U52.1.C2' set U52.1 connect0 U52.1.C5' set U52.1 connect1 U52.1.C2' set U52.1 restype nucleic set U52.1 name "U52" # set FF atom types set U52.1.O3' type OH set U52.1.H3T type HO set U52.1.C5' type CT set U52.1.H5'1 type H1 set U52.1.H5'2 type H1 set U52.1.O4' type OS set U52.1.C4' type CT set U52.1.H4' type H1 set U52.1.C3' type CT set U52.1.H3' type H1 set U52.1.C2' type CT set U52.1.H2' type H1 set U52.1.C1' type CT set U52.1.H1' type "H2" set U52.1.O4 type O set U52.1.C4 type C set U52.1.N3 type NA set U52.1.H3 type H set U52.1.C2 type C set U52.1.O2 type O set U52.1.N1 type "N*" set U52.1.C6 type CM set U52.1.H6 type H4 set U52.1.C5 type CM set U52.1.H5 type HA set U32 name "U32" set U32 head U32.1.C3' set U32 tail U32.1.C2' set U32.1 connect0 U32.1.C3' set U32.1 connect1 U32.1.C2' set U32.1 restype nucleic set U32.1 name "U32" # set FF atom types set U32.1.O5' type OH set U32.1.H5T type HO set U32.1.C5' type CT set U32.1.H5'1 type H1 set U32.1.H5'2 type H1 set U32.1.O4' type OS set U32.1.C4' type CT set U32.1.H4' type H1 set U32.1.C3' type CT set U32.1.H3' type H1 set U32.1.C2' type CT set U32.1.H2' type H1 set U32.1.C1' type CT set U32.1.H1' type "H2" set U32.1.O4 type O set U32.1.C4 type C set U32.1.N3 type NA set U32.1.H3 type H set U32.1.C2 type C set U32.1.O2 type O set U32.1.N1 type "N*" set U32.1.C6 type CM set U32.1.H6 type H4 set U32.1.C5 type CM set U32.1.H5 type HA # ------- Reduced nicotinamide nucleoside fragments ----------- set RN name "RN" # head & tail null set RN.1 connect0 RN.1.C5' set RN.1 connect1 RN.1.C2' set RN.1 restype nucleic set RN.1 name "RN" # set FF atom types set RN.1.O5' type OH set RN.1.H5T type HO set RN.1.O3' type OH set RN.1.H3T type HO set RN.1.C5' type CT set RN.1.H5'1 type H1 set RN.1.H5'2 type H1 set RN.1.O4' type OS set RN.1.C4' type CT set RN.1.H4' type H1 set RN.1.C3' type CT set RN.1.H3' type H1 set RN.1.C2' type CT set RN.1.H2' type H1 set RN.1.O2' type OH set RN.1.H2T type HO set RN.1.C1' type CT set RN.1.H1' type "H2" set RN.1.N9 type N set RN.1.H91 type H set RN.1.H92 type H set RN.1.C7 type C set RN.1.O8 type O set RN.1.N1 type "N*" set RN.1.C2 type CM set RN.1.H2 type H4 set RN.1.C3 type CA set RN.1.C4 type CT set RN.1.H41 type "HC" set RN.1.H42 type "HC" set RN.1.C5 type CA set RN.1.H5 type HA set RN.1.C6 type CM set RN.1.H6 type H4 set RC name "RC" set RC head RC.1.C5' set RC tail RC.1.C2' set RC.1 connect0 RC.1.C5' set RC.1 connect1 RC.1.C2' set RC.1 restype nucleic set RC.1 name "RC" # set FF atom types set RC.1.C5' type CT set RC.1.H5'1 type H1 set RC.1.H5'2 type H1 set RC.1.O4' type OS set RC.1.C4' type CT set RC.1.H4' type H1 set RC.1.C3' type CT set RC.1.H3' type H1 set RC.1.C2' type CT set RC.1.H2' type H1 set RC.1.C1' type CT set RC.1.H1' type "H2" set RC.1.N9 type N set RC.1.H91 type H set RC.1.H92 type H set RC.1.C7 type C set RC.1.O8 type O set RC.1.N1 type "N*" set RC.1.C2 type CM set RC.1.H2 type H4 set RC.1.C3 type CA set RC.1.C4 type CT set RC.1.H41 type "HC" set RC.1.H42 type "HC" set RC.1.C5 type CA set RC.1.H5 type HA set RC.1.C6 type CM set RC.1.H6 type H4 set R5 name "R5" set R5 head R5.1.C5' # tail null set R5.1 connect0 R5.1.C5' set R5.1 connect1 R5.1.C2' set R5.1 restype nucleic set R5.1 name "R5" # set FF atom types set R5.1.O3' type OH set R5.1.H3T type HO set R5.1.C5' type CT set R5.1.H5'1 type H1 set R5.1.H5'2 type H1 set R5.1.O4' type OS set R5.1.C4' type CT set R5.1.H4' type H1 set R5.1.C3' type CT set R5.1.H3' type H1 set R5.1.C2' type CT set R5.1.H2' type H1 set R5.1.O2' type OH set R5.1.H2T type HO set R5.1.C1' type CT set R5.1.H1' type "H2" set R5.1.N9 type N set R5.1.H91 type H set R5.1.H92 type H set R5.1.C7 type C set R5.1.O8 type O set R5.1.N1 type "N*" set R5.1.C2 type CM set R5.1.H2 type H4 set R5.1.C3 type CA set R5.1.C4 type CT set R5.1.H41 type "HC" set R5.1.H42 type "HC" set R5.1.C5 type CA set R5.1.H5 type HA set R5.1.C6 type CM set R5.1.H6 type H4 set R3 name "R3" set R3 head R3.1.C3' # tail null set R3.1 connect0 R3.1.C3' set R3.1 connect1 R3.1.C2' set R3.1 restype nucleic set R3.1 name "R3" # set FF atom types set R3.1.O5' type OH set R3.1.H5T type HO set R3.1.C5' type CT set R3.1.H5'1 type H1 set R3.1.H5'2 type H1 set R3.1.O4' type OS set R3.1.C4' type CT set R3.1.H4' type H1 set R3.1.C3' type CT set R3.1.H3' type H1 set R3.1.C2' type CT set R3.1.H2' type H1 set R3.1.O2' type OH set R3.1.H2T type HO set R3.1.C1' type CT set R3.1.H1' type "H2" set R3.1.N9 type N set R3.1.H91 type H set R3.1.H92 type H set R3.1.C7 type C set R3.1.O8 type O set R3.1.N1 type "N*" set R3.1.C2 type CM set R3.1.H2 type H4 set R3.1.C3 type CA set R3.1.C4 type CT set R3.1.H41 type "HC" set R3.1.H42 type "HC" set R3.1.C5 type CA set R3.1.H5 type HA set R3.1.C6 type CM set R3.1.H6 type H4 set R2 name "R2" set R2 head R2.1.C2' # tail null set R2.1 connect0 R2.1.C2' set R2.1 connect1 R2.1.C3' set R2.1 restype nucleic set R2.1 name "R2" # set FF atom types set R2.1.O5' type OH set R2.1.H5T type HO set R2.1.O3' type OH set R2.1.H3T type HO set R2.1.C5' type CT set R2.1.H5'1 type H1 set R2.1.H5'2 type H1 set R2.1.O4' type OS set R2.1.C4' type CT set R2.1.H4' type H1 set R2.1.C3' type CT set R2.1.H3' type H1 set R2.1.C2' type CT set R2.1.H2' type H1 set R2.1.C1' type CT set R2.1.H1' type "H2" set R2.1.N9 type N set R2.1.H91 type H set R2.1.H92 type H set R2.1.C7 type C set R2.1.O8 type O set R2.1.N1 type "N*" set R2.1.C2 type CM set R2.1.H2 type H4 set R2.1.C3 type CA set R2.1.C4 type CT set R2.1.H41 type "HC" set R2.1.H42 type "HC" set R2.1.C5 type CA set R2.1.H5 type HA set R2.1.C6 type CM set R2.1.H6 type H4 set R53 name "R53" set R53 head R53.1.C5' set R53 tail R53.1.C3' set R53.1 connect0 R53.1.C5' set R53.1 connect1 R53.1.C3' set R53.1 restype nucleic set R53.1 name "R53" # set FF atom types set R53.1.C5' type CT set R53.1.H5'1 type H1 set R53.1.H5'2 type H1 set R53.1.O4' type OS set R53.1.C4' type CT set R53.1.H4' type H1 set R53.1.C3' type CT set R53.1.H3' type H1 set R53.1.C2' type CT set R53.1.H2' type H1 set R53.1.O2' type OH set R53.1.H2T type HO set R53.1.C1' type CT set R53.1.H1' type "H2" set R53.1.N9 type N set R53.1.H91 type H set R53.1.H92 type H set R53.1.C7 type C set R53.1.O8 type O set R53.1.N1 type "N*" set R53.1.C2 type CM set R53.1.H2 type H4 set R53.1.C3 type CA set R53.1.C4 type CT set R53.1.H41 type "HC" set R53.1.H42 type "HC" set R53.1.C5 type CA set R53.1.H5 type HA set R53.1.C6 type CM set R53.1.H6 type H4 set R52 name "R52" set R52 head R52.1.C5' set R52 tail R52.1.C2' set R52.1 connect0 R52.1.C5' set R52.1 connect1 R52.1.C2' set R52.1 restype nucleic set R52.1 name "R52" # set FF atom types set R52.1.O3' type OH set R52.1.H3T type HO set R52.1.C5' type CT set R52.1.H5'1 type H1 set R52.1.H5'2 type H1 set R52.1.O4' type OS set R52.1.C4' type CT set R52.1.H4' type H1 set R52.1.C3' type CT set R52.1.H3' type H1 set R52.1.C2' type CT set R52.1.H2' type H1 set R52.1.C1' type CT set R52.1.H1' type "H2" set R52.1.N9 type N set R52.1.H91 type H set R52.1.H92 type H set R52.1.C7 type C set R52.1.O8 type O set R52.1.N1 type "N*" set R52.1.C2 type CM set R52.1.H2 type H4 set R52.1.C3 type CA set R52.1.C4 type CT set R52.1.H41 type "HC" set R52.1.H42 type "HC" set R52.1.C5 type CA set R52.1.H5 type HA set R52.1.C6 type CM set R52.1.H6 type H4 set R32 name "R32" set R32 head R32.1.C3' set R32 tail R32.1.C2' set R32.1 connect0 R32.1.C3' set R32.1 connect1 R32.1.C2' set R32.1 restype nucleic set R32.1 name "R32" # set FF atom types set R32.1.O5' type OH set R32.1.H5T type HO set R32.1.C5' type CT set R32.1.H5'1 type H1 set R32.1.H5'2 type H1 set R32.1.O4' type OS set R32.1.C4' type CT set R32.1.H4' type H1 set R32.1.C3' type CT set R32.1.H3' type H1 set R32.1.C2' type CT set R32.1.H2' type H1 set R32.1.C1' type CT set R32.1.H1' type "H2" set R32.1.N9 type N set R32.1.H91 type H set R32.1.H92 type H set R32.1.C7 type C set R32.1.O8 type O set R32.1.N1 type "N*" set R32.1.C2 type CM set R32.1.H2 type H4 set R32.1.C3 type CA set R32.1.C4 type CT set R32.1.H41 type "HC" set R32.1.H42 type "HC" set R32.1.C5 type CA set R32.1.H5 type HA set R32.1.C6 type CM set R32.1.H6 type H4 # ------- Nicotinamide nucleoside fragments ----------- set IN name "IN" # head & tail null set IN.1 connect0 IN.1.C5' set IN.1 connect1 IN.1.C2' set IN.1 restype nucleic set IN.1 name "IN" # set FF atom types set IN.1.O5' type OH set IN.1.H5T type HO set IN.1.O3' type OH set IN.1.H3T type HO set IN.1.C5' type CT set IN.1.H5'1 type H1 set IN.1.H5'2 type H1 set IN.1.O4' type OS set IN.1.C4' type CT set IN.1.H4' type H1 set IN.1.C3' type CT set IN.1.H3' type H1 set IN.1.C2' type CT set IN.1.H2' type H1 set IN.1.O2' type OH set IN.1.H2T type HO set IN.1.C1' type CT set IN.1.H1' type "H2" set IN.1.N9 type N set IN.1.H91 type H set IN.1.H92 type H set IN.1.C7 type C set IN.1.O8 type O set IN.1.N1 type "N*" set IN.1.C2 type CM set IN.1.H2 type H4 set IN.1.C3 type CA set IN.1.C4 type CA set IN.1.H4 type HA set IN.1.C5 type CA set IN.1.H5 type HA set IN.1.C6 type CM set IN.1.H6 type H4 set IC name "IC" set IC head IC.1.C5' set IC tail IC.1.C2' set IC.1 connect0 IC.1.C5' set IC.1 connect1 IC.1.C2' set IC.1 restype nucleic set IC.1 name "IC" # set FF atom types set IC.1.C5' type CT set IC.1.H5'1 type H1 set IC.1.H5'2 type H1 set IC.1.O4' type OS set IC.1.C4' type CT set IC.1.H4' type H1 set IC.1.C3' type CT set IC.1.H3' type H1 set IC.1.C2' type CT set IC.1.H2' type H1 set IC.1.C1' type CT set IC.1.H1' type "H2" set IC.1.N9 type N set IC.1.H91 type H set IC.1.H92 type H set IC.1.C7 type C set IC.1.O8 type O set IC.1.N1 type "N*" set IC.1.C2 type CM set IC.1.H2 type H4 set IC.1.C3 type CA set IC.1.C4 type CA set IC.1.H4 type HA set IC.1.C5 type CA set IC.1.H5 type HA set IC.1.C6 type CM set IC.1.H6 type H4 set I5 name "I5" set I5 head I5.1.C5' # tail null set I5.1 connect0 I5.1.C5' set I5.1 connect1 I5.1.C2' set I5.1 restype nucleic set I5.1 name "I5" # set FF atom types set I5.1.O3' type OH set I5.1.H3T type HO set I5.1.C5' type CT set I5.1.H5'1 type H1 set I5.1.H5'2 type H1 set I5.1.O4' type OS set I5.1.C4' type CT set I5.1.H4' type H1 set I5.1.C3' type CT set I5.1.H3' type H1 set I5.1.C2' type CT set I5.1.H2' type H1 set I5.1.O2' type OH set I5.1.H2T type HO set I5.1.C1' type CT set I5.1.H1' type "H2" set I5.1.N9 type N set I5.1.H91 type H set I5.1.H92 type H set I5.1.C7 type C set I5.1.O8 type O set I5.1.N1 type "N*" set I5.1.C2 type CM set I5.1.H2 type H4 set I5.1.C3 type CA set I5.1.C4 type CA set I5.1.H4 type HA set I5.1.C5 type CA set I5.1.H5 type HA set I5.1.C6 type CM set I5.1.H6 type H4 set I3 name "I3" set I3 head I3.1.C3' # tail null set I3.1 connect0 I3.1.C3' set I3.1 connect1 I3.1.C2' set I3.1 restype nucleic set I3.1 name "I3" # set FF atom types set I3.1.O5' type OH set I3.1.H5T type HO set I3.1.C5' type CT set I3.1.H5'1 type H1 set I3.1.H5'2 type H1 set I3.1.O4' type OS set I3.1.C4' type CT set I3.1.H4' type H1 set I3.1.C3' type CT set I3.1.H3' type H1 set I3.1.C2' type CT set I3.1.H2' type H1 set I3.1.O2' type OH set I3.1.H2T type HO set I3.1.C1' type CT set I3.1.H1' type "H2" set I3.1.N9 type N set I3.1.H91 type H set I3.1.H92 type H set I3.1.C7 type C set I3.1.O8 type O set I3.1.N1 type "N*" set I3.1.C2 type CM set I3.1.H2 type H4 set I3.1.C3 type CA set I3.1.C4 type CA set I3.1.H4 type HA set I3.1.C5 type CA set I3.1.H5 type HA set I3.1.C6 type CM set I3.1.H6 type H4 set I2 name "I2" set I2 head I2.1.C2' # tail null set I2.1 connect0 I2.1.C2' set I2.1 connect1 I2.1.C3' set I2.1 restype nucleic set I2.1 name "I2" # set FF atom types set I2.1.O5' type OH set I2.1.H5T type HO set I2.1.O3' type OH set I2.1.H3T type HO set I2.1.C5' type CT set I2.1.H5'1 type H1 set I2.1.H5'2 type H1 set I2.1.O4' type OS set I2.1.C4' type CT set I2.1.H4' type H1 set I2.1.C3' type CT set I2.1.H3' type H1 set I2.1.C2' type CT set I2.1.H2' type H1 set I2.1.C1' type CT set I2.1.H1' type "H2" set I2.1.N9 type N set I2.1.H91 type H set I2.1.H92 type H set I2.1.C7 type C set I2.1.O8 type O set I2.1.N1 type "N*" set I2.1.C2 type CM set I2.1.H2 type H4 set I2.1.C3 type CA set I2.1.C4 type CA set I2.1.H4 type HA set I2.1.C5 type CA set I2.1.H5 type HA set I2.1.C6 type CM set I2.1.H6 type H4 set I53 name "I53" set I53 head I53.1.C5' set I53 tail I53.1.C3' set I53.1 connect0 I53.1.C5' set I53.1 connect1 I53.1.C3' set I53.1 restype nucleic set I53.1 name "I53" # set FF atom types set I53.1.C5' type CT set I53.1.H5'1 type H1 set I53.1.H5'2 type H1 set I53.1.O4' type OS set I53.1.C4' type CT set I53.1.H4' type H1 set I53.1.C3' type CT set I53.1.H3' type H1 set I53.1.C2' type CT set I53.1.H2' type H1 set I53.1.O2' type OH set I53.1.H2T type HO set I53.1.C1' type CT set I53.1.H1' type "H2" set I53.1.N9 type N set I53.1.H91 type H set I53.1.H92 type H set I53.1.C7 type C set I53.1.O8 type O set I53.1.N1 type "N*" set I53.1.C2 type CM set I53.1.H2 type H4 set I53.1.C3 type CA set I53.1.C4 type CA set I53.1.H4 type HA set I53.1.C5 type CA set I53.1.H5 type HA set I53.1.C6 type CM set I53.1.H6 type H4 set I52 name "I52" set I52 head I52.1.C5' set I52 tail I52.1.C2' set I52.1 connect0 I52.1.C5' set I52.1 connect1 I52.1.C2' set I52.1 restype nucleic set I52.1 name "I52" # set FF atom types set I52.1.O3' type OH set I52.1.H3T type HO set I52.1.C5' type CT set I52.1.H5'1 type H1 set I52.1.H5'2 type H1 set I52.1.O4' type OS set I52.1.C4' type CT set I52.1.H4' type H1 set I52.1.C3' type CT set I52.1.H3' type H1 set I52.1.C2' type CT set I52.1.H2' type H1 set I52.1.C1' type CT set I52.1.H1' type "H2" set I52.1.N9 type N set I52.1.H91 type H set I52.1.H92 type H set I52.1.C7 type C set I52.1.O8 type O set I52.1.N1 type "N*" set I52.1.C2 type CM set I52.1.H2 type H4 set I52.1.C3 type CA set I52.1.C4 type CA set I52.1.H4 type HA set I52.1.C5 type CA set I52.1.H5 type HA set I52.1.C6 type CM set I52.1.H6 type H4 set I32 name "I32" set I32 head I32.1.C3' set I32 tail I32.1.C2' set I32.1 connect0 I32.1.C3' set I32.1 connect1 I32.1.C2' set I32.1 restype nucleic set I32.1 name "I32" # set FF atom types set I32.1.O5' type OH set I32.1.H5T type HO set I32.1.C5' type CT set I32.1.H5'1 type H1 set I32.1.H5'2 type H1 set I32.1.O4' type OS set I32.1.C4' type CT set I32.1.H4' type H1 set I32.1.C3' type CT set I32.1.H3' type H1 set I32.1.C2' type CT set I32.1.H2' type H1 set I32.1.C1' type CT set I32.1.H1' type "H2" set I32.1.N9 type N set I32.1.H91 type H set I32.1.H92 type H set I32.1.C7 type C set I32.1.O8 type O set I32.1.N1 type "N*" set I32.1.C2 type CM set I32.1.H2 type H4 set I32.1.C3 type CA set I32.1.C4 type CA set I32.1.H4 type HA set I32.1.C5 type CA set I32.1.H5 type HA set I32.1.C6 type CM set I32.1.H6 type H4 # ------- Riboflavin, FMN & FMNH2 fragments ----------- set LNK name "LNK" set LNK head LNK.1.C5 set LNK tail LNK.1.C1 set LNK.1 connect0 LNK.1.C5 set LNK.1 connect1 LNK.1.C1 set LNK.1 restype undefined set LNK.1 name "LNK" # set FF atom types set LNK.1.C1 type CT set LNK.1.H11 type H1 set LNK.1.H12 type H1 set LNK.1.C2 type CT set LNK.1.H2 type H1 set LNK.1.O2 type OH set LNK.1.HO2 type HO set LNK.1.C3 type CT set LNK.1.H3 type H1 set LNK.1.O3 type OH set LNK.1.HO3 type HO set LNK.1.C4 type CT set LNK.1.H4 type H1 set LNK.1.O4 type OH set LNK.1.HO4 type HO set LNK.1.C5 type CT set LNK.1.H51 type H1 set LNK.1.H52 type H1 set LNO name "LNO" set LNO head LNO.1.O5 set LNO tail LNO.1.C1 set LNO.1 connect0 LNO.1.O5 set LNO.1 connect1 LNO.1.C1 set LNO.1 restype undefined set LNO.1 name "LNO" # set FF atom types set LNO.1.C1 type CT set LNO.1.H11 type H1 set LNO.1.H12 type H1 set LNO.1.C2 type CT set LNO.1.H2 type H1 set LNO.1.O2 type OH set LNO.1.HO2 type HO set LNO.1.C3 type CT set LNO.1.H3 type H1 set LNO.1.O3 type OH set LNO.1.HO3 type HO set LNO.1.C4 type CT set LNO.1.H4 type H1 set LNO.1.O4 type OH set LNO.1.HO4 type HO set LNO.1.C5 type CT set LNO.1.H51 type H1 set LNO.1.H52 type H1 set LNO.1.O5 type OH set LNO.1.HO5 type HO set FLO name "FLO" set FLO head FLO.1.N10 set FLO tail FLO.1.N1 set FLO.1 connect0 FLO.1.N10 set FLO.1 connect1 FLO.1.N1 set FLO.1 restype undefined set FLO.1 name "FLO" # set FF atom types set FLO.1.N1 type NC set FLO.1.C2 type C set FLO.1.O2 type O set FLO.1.N3 type NA set FLO.1.H3 type H set FLO.1.C4 type C set FLO.1.O4 type O set FLO.1.N10 type "N*" set FLO.1.C10A type CB set FLO.1.C4A type CB set FLO.1.N5 type NC set FLO.1.C5A type CB set FLO.1.C9A type CB set FLO.1.C9 type CA set FLO.1.H9 type HA set FLO.1.C8 type CA set FLO.1.C7 type CA set FLO.1.C6 type CA set FLO.1.H6 type HA set FLO.1.C7M type CT set FLO.1.H7M1 type "HC" set FLO.1.H7M2 type "HC" set FLO.1.H7M3 type "HC" set FLO.1.C8M type CT set FLO.1.H8M1 type "HC" set FLO.1.H8M2 type "HC" set FLO.1.H8M3 type "HC" set FLR name "FLR" set FLR head FLR.1.N10 set FLR tail FLR.1.N1 set FLR.1 connect0 FLR.1.N10 set FLR.1 connect1 FLR.1.N1 set FLR.1 restype undefined set FLR.1 name "FLR" # set FF atom types set FLR.1.N1 type NA set FLR.1.H1 type H set FLR.1.C2 type C set FLR.1.O2 type O set FLR.1.N3 type NA set FLR.1.H3 type H set FLR.1.C4 type C set FLR.1.O4 type O set FLR.1.N10 type "N*" set FLR.1.C10A type CB set FLR.1.C4A type CB set FLR.1.N5 type NA set FLR.1.H5 type H set FLR.1.C5A type CB set FLR.1.C9A type CB set FLR.1.C9 type CA set FLR.1.H9 type HA set FLR.1.C8 type CA set FLR.1.C7 type CA set FLR.1.C6 type CA set FLR.1.H6 type HA set FLR.1.C7M type CT set FLR.1.H7M1 type "HC" set FLR.1.H7M2 type "HC" set FLR.1.H7M3 type "HC" set FLR.1.C8M type CT set FLR.1.H8M1 type "HC" set FLR.1.H8M2 type "HC" set FLR.1.H8M3 type "HC" # ------- Co-Enzyme A & Acetyl CoA fragments ----------- set AC1 name "AC1" set AC1 head AC1.1.C1 set AC1 tail AC1.1.C set AC1.1 connect0 AC1.1.C1 set AC1.1 connect1 AC1.1.C set AC1.1 restype undefined set AC1.1 name "AC1" # set FF atom types set AC1.1.C1 type CT set AC1.1.H11 type H1 set AC1.1.H12 type H1 set AC1.1.C2 type CT set AC1.1.C3 type CT set AC1.1.H31 type "HC" set AC1.1.H32 type "HC" set AC1.1.H33 type "HC" set AC1.1.C4 type CT set AC1.1.H41 type "HC" set AC1.1.H42 type "HC" set AC1.1.H43 type "HC" set AC1.1.C5 type CT set AC1.1.H5 type H1 set AC1.1.O5 type OH set AC1.1.HO5 type HO set AC1.1.C type C set AC1.1.O type O set AO1 name "AO1" set AO1 head AO1.1.O1 set AO1 tail AO1.1.C set AO1.1 connect0 AO1.1.O1 set AO1.1 connect1 AO1.1.C set AO1.1 restype undefined set AO1.1 name "AO1" # set FF atom types set AO1.1.O1 type OH set AO1.1.H1 type HO set AO1.1.C1 type CT set AO1.1.H11 type H1 set AO1.1.H12 type H1 set AO1.1.C2 type CT set AO1.1.C3 type CT set AO1.1.H31 type "HC" set AO1.1.H32 type "HC" set AO1.1.H33 type "HC" set AO1.1.C4 type CT set AO1.1.H41 type "HC" set AO1.1.H42 type "HC" set AO1.1.H43 type "HC" set AO1.1.C5 type CT set AO1.1.H5 type H1 set AO1.1.O5 type OH set AO1.1.HO5 type HO set AO1.1.C type C set AO1.1.O type O set AC2 name "AC2" set AC2 head AC2.1.N set AC2 tail AC2.1.C set AC2.1 connect0 AC2.1.N set AC2.1 connect1 AC2.1.C set AC2.1 restype undefined set AC2.1 name "AC2" # set FF atom types set AC2.1.N type N set AC2.1.H type H set AC2.1.C6 type CT set AC2.1.H61 type H1 set AC2.1.H62 type H1 set AC2.1.C7 type CT set AC2.1.H71 type "HC" set AC2.1.H72 type "HC" set AC2.1.C type C set AC2.1.O type O set AC3 name "AC3" set AC3 head AC3.1.N set AC3 tail AC3.1.S set AC3.1 connect0 AC3.1.N set AC3.1 connect1 AC3.1.S set AC3.1 restype undefined set AC3.1 name "AC3" # set FF atom types set AC3.1.N type N set AC3.1.H type H set AC3.1.C8 type CT set AC3.1.H81 type H1 set AC3.1.H82 type H1 set AC3.1.C9 type CT set AC3.1.H91 type H1 set AC3.1.H92 type H1 set AC3.1.S type S set AC3.1.C type C set AC3.1.O type O set AC3.1.CM type CT set AC3.1.HM1 type "HC" set AC3.1.HM2 type "HC" set AC3.1.HM3 type "HC" set AC4 name "AC4" set AC4 head AC4.1.N set AC4 tail AC4.1.SH set AC4.1 connect0 AC4.1.N set AC4.1 connect1 AC4.1.SH set AC4.1 restype undefined set AC4.1 name "AC4" # set FF atom types set AC4.1.N type N set AC4.1.H type H set AC4.1.C8 type CT set AC4.1.H81 type H1 set AC4.1.H82 type H1 set AC4.1.C9 type CT set AC4.1.H91 type H1 set AC4.1.H92 type H1 set AC4.1.SH type SH set AC4.1.HS type HS # ------- 2-deoxy cyclic nucleoside fragments ----------- set CAP name "CAP" # head & tail null set CAP.1 connect0 CAP.1.P set CAP.1 connect1 CAP.1.C2' set CAP.1 restype nucleic set CAP.1 name "CAP" # set FF atom types set CAP.1.P type P set CAP.1.O1P type O2 set CAP.1.O2P type O2 set CAP.1.O5' type OS set CAP.1.O3' type OS set CAP.1.C5' type CT set CAP.1.H5'1 type H1 set CAP.1.H5'2 type H1 set CAP.1.O4' type OS set CAP.1.C4' type CT set CAP.1.H4' type H1 set CAP.1.C3' type CT set CAP.1.H3' type H1 set CAP.1.C2' type CT set CAP.1.H2'1 type "HC" set CAP.1.H2'2 type "HC" set CAP.1.C1' type CT set CAP.1.H1' type "H2" set CAP.1.N6 type N2 set CAP.1.H61 type H set CAP.1.H62 type H set CAP.1.C6 type CA set CAP.1.C5 type CB set CAP.1.N7 type NB set CAP.1.C8 type CK set CAP.1.H8 type "H5" set CAP.1.N9 type "N*" set CAP.1.C4 type CB set CAP.1.N3 type NC set CAP.1.C2 type CQ set CAP.1.H2 type "H5" set CAP.1.N1 type NC # set CCP name "CCP" # head & tail null set CCP.1 connect0 CCP.1.P set CCP.1 connect1 CCP.1.C2' set CCP.1 restype nucleic set CCP.1 name "CCP" # set FF atom types set CCP.1.P type P set CCP.1.O1P type O2 set CCP.1.O2P type O2 set CCP.1.O5' type OS set CCP.1.O3' type OS set CCP.1.C5' type CT set CCP.1.H5'1 type H1 set CCP.1.H5'2 type H1 set CCP.1.O4' type OS set CCP.1.C4' type CT set CCP.1.H4' type H1 set CCP.1.C3' type CT set CCP.1.H3' type H1 set CCP.1.C2' type CT set CCP.1.H2'1 type "HC" set CCP.1.H2'2 type "HC" set CCP.1.C1' type CT set CCP.1.H1' type "H2" set CCP.1.N4 type N2 set CCP.1.H41 type H set CCP.1.H42 type H set CCP.1.C4 type CA set CCP.1.N3 type NC set CCP.1.C2 type C set CCP.1.O2 type O set CCP.1.N1 type "N*" set CCP.1.C6 type CM set CCP.1.H6 type H4 set CCP.1.C5 type CM set CCP.1.H5 type HA set CGP name "CGP" # head & tail null set CGP.1 connect0 CGP.1.P set CGP.1 connect1 CGP.1.C2' set CGP.1 restype nucleic set CGP.1 name "CGP" # set FF atom types set CGP.1.P type P set CGP.1.O1P type O2 set CGP.1.O2P type O2 set CGP.1.O5' type OS set CGP.1.O3' type OS set CGP.1.C5' type CT set CGP.1.H5'1 type H1 set CGP.1.H5'2 type H1 set CGP.1.O4' type OS set CGP.1.C4' type CT set CGP.1.H4' type H1 set CGP.1.C3' type CT set CGP.1.H3' type H1 set CGP.1.C2' type CT set CGP.1.H2'1 type "HC" set CGP.1.H2'2 type "HC" set CGP.1.C1' type CT set CGP.1.H1' type "H2" set CGP.1.N2 type N2 set CGP.1.H21 type H set CGP.1.H22 type H set CGP.1.O6 type O set CGP.1.C6 type C set CGP.1.C5 type CB set CGP.1.N7 type NB set CGP.1.C8 type CK set CGP.1.H8 type "H5" set CGP.1.N9 type "N*" set CGP.1.C4 type CB set CGP.1.N3 type NC set CGP.1.C2 type CA set CGP.1.N1 type NA set CGP.1.H1 type H set CTP name "CTP" # head & tail null set CTP.1 connect0 CTP.1.P set CTP.1 connect1 CTP.1.C2' set CTP.1 restype nucleic set CTP.1 name "CTP" # set FF atom types set CTP.1.P type P set CTP.1.O1P type O2 set CTP.1.O2P type O2 set CTP.1.O5' type OS set CTP.1.O3' type OS set CTP.1.C5' type CT set CTP.1.H5'1 type H1 set CTP.1.H5'2 type H1 set CTP.1.O4' type OS set CTP.1.C4' type CT set CTP.1.H4' type H1 set CTP.1.C3' type CT set CTP.1.H3' type H1 set CTP.1.C2' type CT set CTP.1.H2'1 type "HC" set CTP.1.H2'2 type "HC" set CTP.1.C1' type CT set CTP.1.H1' type "H2" set CTP.1.O4 type O set CTP.1.C4 type C set CTP.1.N3 type NA set CTP.1.H3 type H set CTP.1.C2 type C set CTP.1.O2 type O set CTP.1.N1 type "N*" set CTP.1.C6 type CM set CTP.1.H6 type H4 set CTP.1.C5 type CM set CTP.1.C7 type CT set CTP.1.H71 type "HC" set CTP.1.H72 type "HC" set CTP.1.H73 type "HC" # ------- Cyclic nucleoside fragments ----------- set CBP name "CBP" # head & tail null set CBP.1 connect0 CBP.1.P set CBP.1 connect1 CBP.1.C2' set CBP.1 restype nucleic set CBP.1 name "CBP" # set FF atom types set CBP.1.P type P set CBP.1.O1P type O2 set CBP.1.O2P type O2 set CBP.1.O5' type OS set CBP.1.O3' type OS set CBP.1.C5' type CT set CBP.1.H5'1 type H1 set CBP.1.H5'2 type H1 set CBP.1.O4' type OS set CBP.1.C4' type CT set CBP.1.H4' type H1 set CBP.1.C3' type CT set CBP.1.H3' type H1 set CBP.1.C2' type CT set CBP.1.H2' type H1 set CBP.1.O2' type OH set CBP.1.H2T type HO set CBP.1.C1' type CT set CBP.1.H1' type "H2" set CBP.1.N6 type N2 set CBP.1.H61 type H set CBP.1.H62 type H set CBP.1.C6 type CA set CBP.1.C5 type CB set CBP.1.N7 type NB set CBP.1.C8 type CK set CBP.1.H8 type "H5" set CBP.1.N9 type "N*" set CBP.1.C4 type CB set CBP.1.N3 type NC set CBP.1.C2 type CQ set CBP.1.H2 type "H5" set CBP.1.N1 type NC set CBO name "CBO" set CBO head CBO.1.C2' set CBO tail CBO.1.P set CBO.1 connect0 CBO.1.C2' set CBO.1 connect1 CBO.1.P set CBO.1 restype nucleic set CBO.1 name "CBO" # set FF atom types set CBO.1.P type P set CBO.1.O1P type O2 set CBO.1.O2P type O2 set CBO.1.O5' type OS set CBO.1.O3' type OS set CBO.1.C5' type CT set CBO.1.H5'1 type H1 set CBO.1.H5'2 type H1 set CBO.1.O4' type OS set CBO.1.C4' type CT set CBO.1.H4' type H1 set CBO.1.C3' type CT set CBO.1.H3' type H1 set CBO.1.C2' type CT set CBO.1.H2' type H1 set CBO.1.C1' type CT set CBO.1.H1' type "H2" set CBO.1.N6 type N2 set CBO.1.H61 type H set CBO.1.H62 type H set CBO.1.C6 type CA set CBO.1.C5 type CB set CBO.1.N7 type NB set CBO.1.C8 type CK set CBO.1.H8 type "H5" set CBO.1.N9 type "N*" set CBO.1.C4 type CB set CBO.1.N3 type NC set CBO.1.C2 type CQ set CBO.1.H2 type "H5" set CBO.1.N1 type NC set CDP name "CDP" # head & tail null set CDP.1 connect0 CDP.1.P set CDP.1 connect1 CDP.1.C2' set CDP.1 restype nucleic set CDP.1 name "CDP" # set FF atom types set CDP.1.P type P set CDP.1.O1P type O2 set CDP.1.O2P type O2 set CDP.1.O5' type OS set CDP.1.O3' type OS set CDP.1.C5' type CT set CDP.1.H5'1 type H1 set CDP.1.H5'2 type H1 set CDP.1.O4' type OS set CDP.1.C4' type CT set CDP.1.H4' type H1 set CDP.1.C3' type CT set CDP.1.H3' type H1 set CDP.1.C2' type CT set CDP.1.H2' type H1 set CDP.1.O2' type OH set CDP.1.H2T type HO set CDP.1.C1' type CT set CDP.1.H1' type "H2" set CDP.1.N4 type N2 set CDP.1.H41 type H set CDP.1.H42 type H set CDP.1.C4 type CA set CDP.1.N3 type NC set CDP.1.C2 type C set CDP.1.O2 type O set CDP.1.N1 type "N*" set CDP.1.C6 type CM set CDP.1.H6 type H4 set CDP.1.C5 type CM set CDP.1.H5 type HA set CDO name "CDO" set CDO head CDO.1.C2' set CDO tail CDO.1.P set CDO.1 connect0 CDO.1.C2' set CDO.1 connect1 CDO.1.P set CDO.1 restype nucleic set CDO.1 name "CDO" # set FF atom types set CDO.1.P type P set CDO.1.O1P type O2 set CDO.1.O2P type O2 set CDO.1.O5' type OS set CDO.1.O3' type OS set CDO.1.C5' type CT set CDO.1.H5'1 type H1 set CDO.1.H5'2 type H1 set CDO.1.O4' type OS set CDO.1.C4' type CT set CDO.1.H4' type H1 set CDO.1.C3' type CT set CDO.1.H3' type H1 set CDO.1.C2' type CT set CDO.1.H2' type H1 set CDO.1.C1' type CT set CDO.1.H1' type "H2" set CDO.1.N4 type N2 set CDO.1.H41 type H set CDO.1.H42 type H set CDO.1.C4 type CA set CDO.1.N3 type NC set CDO.1.C2 type C set CDO.1.O2 type O set CDO.1.N1 type "N*" set CDO.1.C6 type CM set CDO.1.H6 type H4 set CDO.1.C5 type CM set CDO.1.H5 type HA set CHP name "CHP" # head & tail null set CHP.1 connect0 CHP.1.P set CHP.1 connect1 CHP.1.C2' set CHP.1 restype nucleic set CHP.1 name "CHP" # set FF atom types set CHP.1.P type P set CHP.1.O1P type O2 set CHP.1.O2P type O2 set CHP.1.O5' type OS set CHP.1.O3' type OS set CHP.1.C5' type CT set CHP.1.H5'1 type H1 set CHP.1.H5'2 type H1 set CHP.1.O4' type OS set CHP.1.C4' type CT set CHP.1.H4' type H1 set CHP.1.C3' type CT set CHP.1.H3' type H1 set CHP.1.C2' type CT set CHP.1.H2' type H1 set CHP.1.O2' type OH set CHP.1.H2T type HO set CHP.1.C1' type CT set CHP.1.H1' type "H2" set CHP.1.N2 type N2 set CHP.1.H21 type H set CHP.1.H22 type H set CHP.1.O6 type O set CHP.1.C6 type C set CHP.1.C5 type CB set CHP.1.N7 type NB set CHP.1.C8 type CK set CHP.1.H8 type "H5" set CHP.1.N9 type "N*" set CHP.1.C4 type CB set CHP.1.N3 type NC set CHP.1.C2 type CA set CHP.1.N1 type NA set CHP.1.H1 type H set CHO name "CHO" set CHO head CHO.1.C2' set CHO tail CHO.1.P set CHO.1 connect0 CHO.1.C2' set CHO.1 connect1 CHO.1.P set CHO.1 restype nucleic set CHO.1 name "CHO" # set FF atom types set CHO.1.P type P set CHO.1.O1P type O2 set CHO.1.O2P type O2 set CHO.1.O5' type OS set CHO.1.O3' type OS set CHO.1.C5' type CT set CHO.1.H5'1 type H1 set CHO.1.H5'2 type H1 set CHO.1.O4' type OS set CHO.1.C4' type CT set CHO.1.H4' type H1 set CHO.1.C3' type CT set CHO.1.H3' type H1 set CHO.1.C2' type CT set CHO.1.H2' type H1 set CHO.1.C1' type CT set CHO.1.H1' type "H2" set CHO.1.N2 type N2 set CHO.1.H21 type H set CHO.1.H22 type H set CHO.1.O6 type O set CHO.1.C6 type C set CHO.1.C5 type CB set CHO.1.N7 type NB set CHO.1.C8 type CK set CHO.1.H8 type "H5" set CHO.1.N9 type "N*" set CHO.1.C4 type CB set CHO.1.N3 type NC set CHO.1.C2 type CA set CHO.1.N1 type NA set CHO.1.H1 type H set CUP name "CUP" # head & tail null set CUP.1 connect0 CUP.1.P set CUP.1 connect1 CUP.1.C2' set CUP.1 restype nucleic set CUP.1 name "CUP" # set FF atom types set CUP.1.P type P set CUP.1.O1P type O2 set CUP.1.O2P type O2 set CUP.1.O5' type OS set CUP.1.O3' type OS set CUP.1.C5' type CT set CUP.1.H5'1 type H1 set CUP.1.H5'2 type H1 set CUP.1.O4' type OS set CUP.1.C4' type CT set CUP.1.H4' type H1 set CUP.1.C3' type CT set CUP.1.H3' type H1 set CUP.1.C2' type CT set CUP.1.H2' type H1 set CUP.1.O2' type OH set CUP.1.H2T type HO set CUP.1.C1' type CT set CUP.1.H1' type "H2" set CUP.1.O4 type O set CUP.1.C4 type C set CUP.1.N3 type NA set CUP.1.H3 type H set CUP.1.C2 type C set CUP.1.O2 type O set CUP.1.N1 type "N*" set CUP.1.C6 type CM set CUP.1.H6 type H4 set CUP.1.C5 type CM set CUP.1.H5 type HA set CUO name "CUO" set CUO head CUO.1.C2' set CUO tail CUO.1.P set CUO.1 connect0 CUO.1.C2' set CUO.1 connect1 CUO.1.P set CUO.1 restype nucleic set CUO.1 name "CUO" # set FF atom types set CUO.1.P type P set CUO.1.O1P type O2 set CUO.1.O2P type O2 set CUO.1.O5' type OS set CUO.1.O3' type OS set CUO.1.C5' type CT set CUO.1.H5'1 type H1 set CUO.1.H5'2 type H1 set CUO.1.O4' type OS set CUO.1.C4' type CT set CUO.1.H4' type H1 set CUO.1.C3' type CT set CUO.1.H3' type H1 set CUO.1.C2' type CT set CUO.1.H2' type H1 set CUO.1.C1' type CT set CUO.1.H1' type "H2" set CUO.1.O4 type O set CUO.1.C4 type C set CUO.1.N3 type NA set CUO.1.H3 type H set CUO.1.C2 type C set CUO.1.O2 type O set CUO.1.N1 type "N*" set CUO.1.C6 type CM set CUO.1.H6 type H4 set CUO.1.C5 type CM set CUO.1.H5 type HA c POP c P1 c P1M c P2M c AN c AC c A5 c A3 c CN c CC c C5 c C3 c GN c GC c G5 c G3 c TN c TC c T5 c T3 c BN c BC c B5 c B3 c B2 c B53 c B52 c B32 c DN c DC c D5 c D3 c D2 c D53 c D52 c D32 c HN c HC c H5 c H3 c H2 c H53 c H52 c H32 c UN c UC c U5 c U3 c U2 c U53 c U52 c U32 c RN c RC c R5 c R3 c R2 c R53 c R52 c R32 c IN c IC c I5 c I3 c I2 c I53 c I52 c I32 c LNK c LNO c FLO c FLR c AC1 c AO1 c AC2 c AC3 c AC4 c CAP c CCP c CGP c CTP c CBP c CBO c CDP c CDO c CHP c CHO c CUP c CUO saveoff POP q4md-forcefieldtools-cofactors.off saveoff P1 q4md-forcefieldtools-cofactors.off saveoff P1M q4md-forcefieldtools-cofactors.off saveoff P2M q4md-forcefieldtools-cofactors.off saveoff AN q4md-forcefieldtools-cofactors.off saveoff AC q4md-forcefieldtools-cofactors.off saveoff A5 q4md-forcefieldtools-cofactors.off saveoff A3 q4md-forcefieldtools-cofactors.off saveoff CN q4md-forcefieldtools-cofactors.off saveoff CC q4md-forcefieldtools-cofactors.off saveoff C5 q4md-forcefieldtools-cofactors.off saveoff C3 q4md-forcefieldtools-cofactors.off saveoff GN q4md-forcefieldtools-cofactors.off saveoff GC q4md-forcefieldtools-cofactors.off saveoff G5 q4md-forcefieldtools-cofactors.off saveoff G3 q4md-forcefieldtools-cofactors.off saveoff TN q4md-forcefieldtools-cofactors.off saveoff TC q4md-forcefieldtools-cofactors.off saveoff T5 q4md-forcefieldtools-cofactors.off saveoff T3 q4md-forcefieldtools-cofactors.off saveoff BN q4md-forcefieldtools-cofactors.off saveoff BC q4md-forcefieldtools-cofactors.off saveoff B5 q4md-forcefieldtools-cofactors.off saveoff B3 q4md-forcefieldtools-cofactors.off saveoff B2 q4md-forcefieldtools-cofactors.off saveoff B53 q4md-forcefieldtools-cofactors.off saveoff B52 q4md-forcefieldtools-cofactors.off saveoff B32 q4md-forcefieldtools-cofactors.off saveoff DN q4md-forcefieldtools-cofactors.off saveoff DC q4md-forcefieldtools-cofactors.off saveoff D5 q4md-forcefieldtools-cofactors.off saveoff D3 q4md-forcefieldtools-cofactors.off saveoff D2 q4md-forcefieldtools-cofactors.off saveoff D53 q4md-forcefieldtools-cofactors.off saveoff D52 q4md-forcefieldtools-cofactors.off saveoff D32 q4md-forcefieldtools-cofactors.off saveoff HN q4md-forcefieldtools-cofactors.off saveoff HC q4md-forcefieldtools-cofactors.off saveoff H5 q4md-forcefieldtools-cofactors.off saveoff H3 q4md-forcefieldtools-cofactors.off saveoff H2 q4md-forcefieldtools-cofactors.off saveoff H53 q4md-forcefieldtools-cofactors.off saveoff H52 q4md-forcefieldtools-cofactors.off saveoff H32 q4md-forcefieldtools-cofactors.off saveoff UN q4md-forcefieldtools-cofactors.off saveoff UC q4md-forcefieldtools-cofactors.off saveoff U5 q4md-forcefieldtools-cofactors.off saveoff U3 q4md-forcefieldtools-cofactors.off saveoff U2 q4md-forcefieldtools-cofactors.off saveoff U53 q4md-forcefieldtools-cofactors.off saveoff U52 q4md-forcefieldtools-cofactors.off saveoff U32 q4md-forcefieldtools-cofactors.off saveoff RN q4md-forcefieldtools-cofactors.off saveoff RC q4md-forcefieldtools-cofactors.off saveoff R5 q4md-forcefieldtools-cofactors.off saveoff R3 q4md-forcefieldtools-cofactors.off saveoff R2 q4md-forcefieldtools-cofactors.off saveoff R53 q4md-forcefieldtools-cofactors.off saveoff R52 q4md-forcefieldtools-cofactors.off saveoff R32 q4md-forcefieldtools-cofactors.off saveoff IN q4md-forcefieldtools-cofactors.off saveoff IC q4md-forcefieldtools-cofactors.off saveoff I5 q4md-forcefieldtools-cofactors.off saveoff I3 q4md-forcefieldtools-cofactors.off saveoff I2 q4md-forcefieldtools-cofactors.off saveoff I53 q4md-forcefieldtools-cofactors.off saveoff I52 q4md-forcefieldtools-cofactors.off saveoff I32 q4md-forcefieldtools-cofactors.off saveoff LNK q4md-forcefieldtools-cofactors.off saveoff LNO q4md-forcefieldtools-cofactors.off saveoff FLO q4md-forcefieldtools-cofactors.off saveoff FLR q4md-forcefieldtools-cofactors.off saveoff AC1 q4md-forcefieldtools-cofactors.off saveoff AO1 q4md-forcefieldtools-cofactors.off saveoff AC2 q4md-forcefieldtools-cofactors.off saveoff AC3 q4md-forcefieldtools-cofactors.off saveoff AC4 q4md-forcefieldtools-cofactors.off saveoff CAP q4md-forcefieldtools-cofactors.off saveoff CCP q4md-forcefieldtools-cofactors.off saveoff CGP q4md-forcefieldtools-cofactors.off saveoff CTP q4md-forcefieldtools-cofactors.off saveoff CBP q4md-forcefieldtools-cofactors.off saveoff CBO q4md-forcefieldtools-cofactors.off saveoff CDP q4md-forcefieldtools-cofactors.off saveoff CDO q4md-forcefieldtools-cofactors.off saveoff CHP q4md-forcefieldtools-cofactors.off saveoff CHO q4md-forcefieldtools-cofactors.off saveoff CUP q4md-forcefieldtools-cofactors.off saveoff CUO q4md-forcefieldtools-cofactors.off # Now let's build the cofactors # 1) Let's start by AMP, ADP, ATP, AQP and even more... # One can - select a 5', 3' and/or 2' position of ribose for adding the "phosphate system" # - choose a P1M (-1) or P2M (-2) terminal phosphate group # - add as many as P1 central phosphate groups: # i.e. (P1M|P2M)(P1)nX5 n = integer, X = dA, dC, dG, dT, A, C, G or U # (A, C, G, T, B, D, H U) # or (P1M|P2M)(P1)nX3 n = integer, X = dA, dC, dG, dT, A, C, G or U # or (P1M|P2M)(P1)nX2 n = integer, X = dA, dC, dG, dT, A, C, G or U # or (P1M|P2M)(P1)n(P1M|P2M)(P1)nX53 n = integer, X = dA, dC, dG, dT, A, C, G or U # or (P1M|P2M)(P1)n(P1M|P2M)(P1)nX52 n = integer, X = dA, dC, dG, dT, A, C, G or U # or (P1M|P2M)(P1)n(P1M|P2M)(P1)nX32 n = integer, X = dA, dC, dG, dT, A, C, G or U # or (P1M|P2M)(P1)n(P1M|P2M)(P1)n(P1M|P2M)(P1)nXC n = integer, X = dA, dC, dG, dT, A, C, G or U # # A'X'P by default means the phosphate is linked to the 5' ribose position dAMP1 = seq {P1M A5} dAMP2 = seq {P2M A5} dADP1 = seq {P1M P1 A5} dADP2 = seq {P2M P1 A5} dATP1 = seq {P1M P1 P1 A5} dATP2 = seq {P2M P1 P1 A5} dAQP1 = seq {P1M P1 P1 P1 A5} dAQP2 = seq {P2M P1 P1 P1 A5} AMP1 = seq {P1M B5} AMP2 = seq {P2M B5} ADP1 = seq {P1M P1 B5} ADP2 = seq {P2M P1 B5} ATP1 = seq {P1M P1 P1 B5} ATP2 = seq {P2M P1 P1 B5} AQP1 = seq {P1M P1 P1 P1 B5} AQP2 = seq {P2M P1 P1 P1 B5} # For fun... dA10P2 = seq {P2M P1 P1 P1 P1 P1 P1 P1 P1 P1 A5} A10P2 = seq {P2M P1 P1 P1 P1 P1 P1 P1 P1 P1 B5} dCMP1 = seq {P1M C5} dCMP2 = seq {P2M C5} dCDP1 = seq {P1M P1 C5} dCDP2 = seq {P2M P1 C5} dCTP1 = seq {P1M P1 P1 C5} dCTP2 = seq {P2M P1 P1 C5} dCQP1 = seq {P1M P1 P1 P1 C5} dCQP2 = seq {P2M P1 P1 P1 C5} CMP1 = seq {P1M D5} CMP2 = seq {P2M D5} CDP1 = seq {P1M P1 D5} CDP2 = seq {P2M P1 D5} CTP1 = seq {P1M P1 P1 D5} CTP2 = seq {P2M P1 P1 D5} CQP1 = seq {P1M P1 P1 P1 D5} CQP2 = seq {P2M P1 P1 P1 D5} dGMP1 = seq {P1M G5} dGMP2 = seq {P2M G5} dGDP1 = seq {P1M P1 G5} dGDP2 = seq {P2M P1 G5} dGTP1 = seq {P1M P1 P1 G5} dGTP2 = seq {P2M P1 P1 G5} dGQP1 = seq {P1M P1 P1 P1 G5} dGQP2 = seq {P2M P1 P1 P1 G5} GMP1 = seq {P1M H5} GMP2 = seq {P2M H5} GDP1 = seq {P1M P1 H5} GDP2 = seq {P2M P1 H5} GTP1 = seq {P1M P1 P1 H5} GTP2 = seq {P2M P1 P1 H5} GQP1 = seq {P1M P1 P1 P1 H5} GQP2 = seq {P2M P1 P1 P1 H5} dTMP1 = seq {P1M T5} dTMP2 = seq {P2M T5} dTDP1 = seq {P1M P1 T5} dTDP2 = seq {P2M P1 T5} dTTP1 = seq {P1M P1 P1 T5} dTTP2 = seq {P2M P1 P1 T5} dTQP1 = seq {P1M P1 P1 P1 T5} dTQP2 = seq {P2M P1 P1 P1 T5} UMP1 = seq {P1M U5} UMP2 = seq {P2M U5} UDP1 = seq {P1M P1 U5} UDP2 = seq {P2M P1 U5} UTP1 = seq {P1M P1 P1 U5} UTP2 = seq {P2M P1 P1 U5} UQP1 = seq {P1M P1 P1 P1 U5} UQP2 = seq {P2M P1 P1 P1 U5} # Just, generate more 'understandable' initial geometries # Change the dihedral values if you do not like them... i dADP1 { 1 2 } {{ OH P OR P 180 }} i dADP1 { 1 2 } {{ P OR P OR 180 }} i dADP1 { 2 3 } {{ OP2 P OR C5' 60 }} i ADP1 { 1 2 } {{ OH P OR P 180 }} i ADP1 { 1 2 } {{ P OR P OR 180 }} i ADP1 { 2 3 } {{ OP2 P OR C5' 60 }} i dATP1 { 1 2 } {{ OH P OR P 180 }} i dATP1 { 1 2 } {{ P OR P OR 180 }} i dATP1 { 2 3 } {{ OP2 P OR P 60 }} i dATP1 { 2 3 } {{ P OR P OR 180 }} i dATP1 { 3 4 } {{ OP2 P OR C5' 60 }} i ATP1 { 1 2 } {{ OH P OR P 180 }} i ATP1 { 1 2 } {{ P OR P OR 180 }} i ATP1 { 2 3 } {{ OP2 P OR P 60 }} i ATP1 { 2 3 } {{ P OR P OR 180 }} i ATP1 { 3 4 } {{ OP2 P OR C5' 60 }} i dAQP1 { 1 2 } {{ OH P OR P 180 }} i dAQP1 { 1 2 } {{ P OR P OR 180 }} i dAQP1 { 2 3 } {{ OP2 P OR P 60 }} i dAQP1 { 2 3 } {{ P OR P OR 180 }} i dAQP1 { 3 4 } {{ OP2 P OR P 60 }} i dAQP1 { 3 4 } {{ P OR P OR 180 }} i dAQP1 { 4 5 } {{ OP2 P OR C5' 60 }} i AQP1 { 1 2 } {{ OH P OR P 180 }} i AQP1 { 1 2 } {{ P OR P OR 180 }} i AQP1 { 2 3 } {{ OP2 P OR P 60 }} i AQP1 { 2 3 } {{ P OR P OR 180 }} i AQP1 { 3 4 } {{ OP2 P OR P 60 }} i AQP1 { 3 4 } {{ P OR P OR 180 }} i AQP1 { 4 5 } {{ OP2 P OR C5' 60 }} i dADP2 { 1 2 } {{ OP1 P OR P 180 }} i dADP2 { 1 2 } {{ P OR P OR 180 }} i dADP2 { 1 2 } {{ OP2 P OR C5' 60 }} i ADP2 { 1 2 } {{ OP1 P OR P 180 }} i ADP2 { 1 2 } {{ P OR P OR 180 }} i ADP2 { 1 2 } {{ OP2 P OR C5' 60 }} i dATP2 { 1 2 } {{ OP1 P OR P 180 }} i dATP2 { 1 2 } {{ P OR P OR 180 }} i dATP2 { 2 3 } {{ OP2 P OR P 60 }} i dATP2 { 2 3 } {{ P OR P OR 180 }} i dATP2 { 3 4 } {{ OP2 P OR C5' 60 }} i ATP2 { 1 2 } {{ OP1 P OR P 180 }} i ATP2 { 1 2 } {{ P OR P OR 180 }} i ATP2 { 2 3 } {{ OP2 P OR P 60 }} i ATP2 { 2 3 } {{ P OR P OR 180 }} i ATP2 { 3 4 } {{ OP2 P OR C5' 60 }} i dAQP2 { 1 2 } {{ OP1 P OR P 180 }} i dAQP2 { 1 2 } {{ P OR P OR 180 }} i dAQP2 { 2 3 } {{ OP2 P OR P 60 }} i dAQP2 { 2 3 } {{ P OR P OR 180 }} i dAQP2 { 3 4 } {{ OP2 P OR P 60 }} i dAQP2 { 3 4 } {{ P OR P OR 180 }} i dAQP2 { 4 5 } {{ OP2 P OR C5' 60 }} i AQP2 { 1 2 } {{ OP1 P OR P 180 }} i AQP2 { 1 2 } {{ P OR P OR 180 }} i AQP2 { 2 3 } {{ OP2 P OR P 60 }} i AQP2 { 2 3 } {{ P OR P OR 180 }} i AQP2 { 3 4 } {{ OP2 P OR P 60 }} i AQP2 { 3 4 } {{ P OR P OR 180 }} i AQP2 { 4 5 } {{ OP2 P OR C5' 60 }} # For fun... dA10P2BIS = copy dA10P2 i dA10P2 { 1 2 } {{ OP1 P OR P 180 }} i dA10P2 { 1 2 } {{ P OR P OR 180 }} i dA10P2 { 2 3 } {{ OP2 P OR P 60 }} i dA10P2 { 2 3 } {{ P OR P OR 180 }} i dA10P2 { 3 4 } {{ OP2 P OR P 60 }} i dA10P2 { 3 4 } {{ P OR P OR 180 }} i dA10P2 { 4 5 } {{ OP2 P OR P 60 }} i dA10P2 { 4 5 } {{ P OR P OR 180 }} i dA10P2 { 5 6 } {{ OP2 P OR P 60 }} i dA10P2 { 5 6 } {{ P OR P OR 180 }} i dA10P2 { 6 7 } {{ OP2 P OR P 60 }} i dA10P2 { 6 7 } {{ P OR P OR 180 }} i dA10P2 { 7 8 } {{ OP2 P OR P 60 }} i dA10P2 { 7 8 } {{ P OR P OR 180 }} i dA10P2 { 8 9 } {{ OP2 P OR P 60 }} i dA10P2 { 8 9 } {{ P OR P OR 180 }} i dA10P2 { 9 10 } {{ OP2 P OR P 60 }} i dA10P2 { 9 10 } {{ P OR P OR 180 }} i dA10P2 { 10 11 } {{ OP2 P OR C5' 60 }} A10P2BIS = copy A10P2 i A10P2 { 1 2 } {{ OP1 P OR P 180 }} i A10P2 { 1 2 } {{ P OR P OR 180 }} i A10P2 { 2 3 } {{ OP2 P OR P 60 }} i A10P2 { 2 3 } {{ P OR P OR 180 }} i A10P2 { 3 4 } {{ OP2 P OR P 60 }} i A10P2 { 3 4 } {{ P OR P OR 180 }} i A10P2 { 4 5 } {{ OP2 P OR P 60 }} i A10P2 { 4 5 } {{ P OR P OR 180 }} i A10P2 { 5 6 } {{ OP2 P OR P 60 }} i A10P2 { 5 6 } {{ P OR P OR 180 }} i A10P2 { 6 7 } {{ OP2 P OR P 60 }} i A10P2 { 6 7 } {{ P OR P OR 180 }} i A10P2 { 7 8 } {{ OP2 P OR P 60 }} i A10P2 { 7 8 } {{ P OR P OR 180 }} i A10P2 { 8 9 } {{ OP2 P OR P 60 }} i A10P2 { 8 9 } {{ P OR P OR 180 }} i A10P2 { 9 10 } {{ OP2 P OR P 60 }} i A10P2 { 9 10 } {{ P OR P OR 180 }} i A10P2 { 10 11 } {{ OP2 P OR C5' 60 }} # edit A10P2 & A10P2BIS for comparison to see what has been done... # ------------------------------------- i dCDP1 { 1 2 } {{ OH P OR P 180 }} i dCDP1 { 1 2 } {{ P OR P OR 180 }} i dCDP1 { 2 3 } {{ OP2 P OR C5' 60 }} i CDP1 { 1 2 } {{ OH P OR P 180 }} i CDP1 { 1 2 } {{ P OR P OR 180 }} i CDP1 { 2 3 } {{ OP2 P OR C5' 60 }} i dCTP1 { 1 2 } {{ OH P OR P 180 }} i dCTP1 { 1 2 } {{ P OR P OR 180 }} i dCTP1 { 2 3 } {{ OP2 P OR P 60 }} i dCTP1 { 2 3 } {{ P OR P OR 180 }} i dCTP1 { 3 4 } {{ OP2 P OR C5' 60 }} i CTP1 { 1 2 } {{ OH P OR P 180 }} i CTP1 { 1 2 } {{ P OR P OR 180 }} i CTP1 { 2 3 } {{ OP2 P OR P 60 }} i CTP1 { 2 3 } {{ P OR P OR 180 }} i CTP1 { 3 4 } {{ OP2 P OR C5' 60 }} i dCQP1 { 1 2 } {{ OH P OR P 180 }} i dCQP1 { 1 2 } {{ P OR P OR 180 }} i dCQP1 { 2 3 } {{ OP2 P OR P 60 }} i dCQP1 { 2 3 } {{ P OR P OR 180 }} i dCQP1 { 3 4 } {{ OP2 P OR P 60 }} i dCQP1 { 3 4 } {{ P OR P OR 180 }} i dCQP1 { 4 5 } {{ OP2 P OR C5' 60 }} i CQP1 { 1 2 } {{ OH P OR P 180 }} i CQP1 { 1 2 } {{ P OR P OR 180 }} i CQP1 { 2 3 } {{ OP2 P OR P 60 }} i CQP1 { 2 3 } {{ P OR P OR 180 }} i CQP1 { 3 4 } {{ OP2 P OR P 60 }} i CQP1 { 3 4 } {{ P OR P OR 180 }} i CQP1 { 4 5 } {{ OP2 P OR C5' 60 }} i dCDP2 { 1 2 } {{ OP1 P OR P 180 }} i dCDP2 { 1 2 } {{ P OR P OR 180 }} i dCDP2 { 1 2 } {{ OP2 P OR C5' 60 }} i CDP2 { 1 2 } {{ OP1 P OR P 180 }} i CDP2 { 1 2 } {{ P OR P OR 180 }} i CDP2 { 1 2 } {{ OP2 P OR C5' 60 }} i dCTP2 { 1 2 } {{ OP1 P OR P 180 }} i dCTP2 { 1 2 } {{ P OR P OR 180 }} i dCTP2 { 2 3 } {{ OP2 P OR P 60 }} i dCTP2 { 2 3 } {{ P OR P OR 180 }} i dCTP2 { 3 4 } {{ OP2 P OR C5' 60 }} i CTP2 { 1 2 } {{ OP1 P OR P 180 }} i CTP2 { 1 2 } {{ P OR P OR 180 }} i CTP2 { 2 3 } {{ OP2 P OR P 60 }} i CTP2 { 2 3 } {{ P OR P OR 180 }} i CTP2 { 3 4 } {{ OP2 P OR C5' 60 }} i dCQP2 { 1 2 } {{ OP1 P OR P 180 }} i dCQP2 { 1 2 } {{ P OR P OR 180 }} i dCQP2 { 2 3 } {{ OP2 P OR P 60 }} i dCQP2 { 2 3 } {{ P OR P OR 180 }} i dCQP2 { 3 4 } {{ OP2 P OR P 60 }} i dCQP2 { 3 4 } {{ P OR P OR 180 }} i dCQP2 { 4 5 } {{ OP2 P OR C5' 60 }} i CQP2 { 1 2 } {{ OP1 P OR P 180 }} i CQP2 { 1 2 } {{ P OR P OR 180 }} i CQP2 { 2 3 } {{ OP2 P OR P 60 }} i CQP2 { 2 3 } {{ P OR P OR 180 }} i CQP2 { 3 4 } {{ OP2 P OR P 60 }} i CQP2 { 3 4 } {{ P OR P OR 180 }} i CQP2 { 4 5 } {{ OP2 P OR C5' 60 }} # ------------------------------------- i dGDP1 { 1 2 } {{ OH P OR P 180 }} i dGDP1 { 1 2 } {{ P OR P OR 180 }} i dGDP1 { 2 3 } {{ OP2 P OR C5' 60 }} i GDP1 { 1 2 } {{ OH P OR P 180 }} i GDP1 { 1 2 } {{ P OR P OR 180 }} i GDP1 { 2 3 } {{ OP2 P OR C5' 60 }} i dGTP1 { 1 2 } {{ OH P OR P 180 }} i dGTP1 { 1 2 } {{ P OR P OR 180 }} i dGTP1 { 2 3 } {{ OP2 P OR P 60 }} i dGTP1 { 2 3 } {{ P OR P OR 180 }} i dGTP1 { 3 4 } {{ OP2 P OR C5' 60 }} i GTP1 { 1 2 } {{ OH P OR P 180 }} i GTP1 { 1 2 } {{ P OR P OR 180 }} i GTP1 { 2 3 } {{ OP2 P OR P 60 }} i GTP1 { 2 3 } {{ P OR P OR 180 }} i GTP1 { 3 4 } {{ OP2 P OR C5' 60 }} i dGQP1 { 1 2 } {{ OH P OR P 180 }} i dGQP1 { 1 2 } {{ P OR P OR 180 }} i dGQP1 { 2 3 } {{ OP2 P OR P 60 }} i dGQP1 { 2 3 } {{ P OR P OR 180 }} i dGQP1 { 3 4 } {{ OP2 P OR P 60 }} i dGQP1 { 3 4 } {{ P OR P OR 180 }} i dGQP1 { 4 5 } {{ OP2 P OR C5' 60 }} i GQP1 { 1 2 } {{ OH P OR P 180 }} i GQP1 { 1 2 } {{ P OR P OR 180 }} i GQP1 { 2 3 } {{ OP2 P OR P 60 }} i GQP1 { 2 3 } {{ P OR P OR 180 }} i GQP1 { 3 4 } {{ OP2 P OR P 60 }} i GQP1 { 3 4 } {{ P OR P OR 180 }} i GQP1 { 4 5 } {{ OP2 P OR C5' 60 }} i dGDP2 { 1 2 } {{ OP1 P OR P 180 }} i dGDP2 { 1 2 } {{ P OR P OR 180 }} i dGDP2 { 1 2 } {{ OP2 P OR C5' 60 }} i GDP2 { 1 2 } {{ OP1 P OR P 180 }} i GDP2 { 1 2 } {{ P OR P OR 180 }} i GDP2 { 1 2 } {{ OP2 P OR C5' 60 }} i dGTP2 { 1 2 } {{ OP1 P OR P 180 }} i dGTP2 { 1 2 } {{ P OR P OR 180 }} i dGTP2 { 2 3 } {{ OP2 P OR P 60 }} i dGTP2 { 2 3 } {{ P OR P OR 180 }} i dGTP2 { 3 4 } {{ OP2 P OR C5' 60 }} i GTP2 { 1 2 } {{ OP1 P OR P 180 }} i GTP2 { 1 2 } {{ P OR P OR 180 }} i GTP2 { 2 3 } {{ OP2 P OR P 60 }} i GTP2 { 2 3 } {{ P OR P OR 180 }} i GTP2 { 3 4 } {{ OP2 P OR C5' 60 }} i dGQP2 { 1 2 } {{ OP1 P OR P 180 }} i dGQP2 { 1 2 } {{ P OR P OR 180 }} i dGQP2 { 2 3 } {{ OP2 P OR P 60 }} i dGQP2 { 2 3 } {{ P OR P OR 180 }} i dGQP2 { 3 4 } {{ OP2 P OR P 60 }} i dGQP2 { 3 4 } {{ P OR P OR 180 }} i dGQP2 { 4 5 } {{ OP2 P OR C5' 60 }} i GQP2 { 1 2 } {{ OP1 P OR P 180 }} i GQP2 { 1 2 } {{ P OR P OR 180 }} i GQP2 { 2 3 } {{ OP2 P OR P 60 }} i GQP2 { 2 3 } {{ P OR P OR 180 }} i GQP2 { 3 4 } {{ OP2 P OR P 60 }} i GQP2 { 3 4 } {{ P OR P OR 180 }} i GQP2 { 4 5 } {{ OP2 P OR C5' 60 }} # ------------------------------------- i dTDP1 { 1 2 } {{ OH P OR P 180 }} i dTDP1 { 1 2 } {{ P OR P OR 180 }} i dTDP1 { 2 3 } {{ OP2 P OR C5' 60 }} i UDP1 { 1 2 } {{ OH P OR P 180 }} i UDP1 { 1 2 } {{ P OR P OR 180 }} i UDP1 { 2 3 } {{ OP2 P OR C5' 60 }} i dTTP1 { 1 2 } {{ OH P OR P 180 }} i dTTP1 { 1 2 } {{ P OR P OR 180 }} i dTTP1 { 2 3 } {{ OP2 P OR P 60 }} i dTTP1 { 2 3 } {{ P OR P OR 180 }} i dTTP1 { 3 4 } {{ OP2 P OR C5' 60 }} i UTP1 { 1 2 } {{ OH P OR P 180 }} i UTP1 { 1 2 } {{ P OR P OR 180 }} i UTP1 { 2 3 } {{ OP2 P OR P 60 }} i UTP1 { 2 3 } {{ P OR P OR 180 }} i UTP1 { 3 4 } {{ OP2 P OR C5' 60 }} i dTQP1 { 1 2 } {{ OH P OR P 180 }} i dTQP1 { 1 2 } {{ P OR P OR 180 }} i dTQP1 { 2 3 } {{ OP2 P OR P 60 }} i dTQP1 { 2 3 } {{ P OR P OR 180 }} i dTQP1 { 3 4 } {{ OP2 P OR P 60 }} i dTQP1 { 3 4 } {{ P OR P OR 180 }} i dTQP1 { 4 5 } {{ OP2 P OR C5' 60 }} i UQP1 { 1 2 } {{ OH P OR P 180 }} i UQP1 { 1 2 } {{ P OR P OR 180 }} i UQP1 { 2 3 } {{ OP2 P OR P 60 }} i UQP1 { 2 3 } {{ P OR P OR 180 }} i UQP1 { 3 4 } {{ OP2 P OR P 60 }} i UQP1 { 3 4 } {{ P OR P OR 180 }} i UQP1 { 4 5 } {{ OP2 P OR C5' 60 }} i dTDP2 { 1 2 } {{ OP1 P OR P 180 }} i dTDP2 { 1 2 } {{ P OR P OR 180 }} i dTDP2 { 1 2 } {{ OP2 P OR C5' 60 }} i UDP2 { 1 2 } {{ OP1 P OR P 180 }} i UDP2 { 1 2 } {{ P OR P OR 180 }} i UDP2 { 1 2 } {{ OP2 P OR C5' 60 }} i dTTP2 { 1 2 } {{ OP1 P OR P 180 }} i dTTP2 { 1 2 } {{ P OR P OR 180 }} i dTTP2 { 2 3 } {{ OP2 P OR P 60 }} i dTTP2 { 2 3 } {{ P OR P OR 180 }} i dTTP2 { 3 4 } {{ OP2 P OR C5' 60 }} i UTP2 { 1 2 } {{ OP1 P OR P 180 }} i UTP2 { 1 2 } {{ P OR P OR 180 }} i UTP2 { 2 3 } {{ OP2 P OR P 60 }} i UTP2 { 2 3 } {{ P OR P OR 180 }} i UTP2 { 3 4 } {{ OP2 P OR C5' 60 }} i dTQP2 { 1 2 } {{ OP1 P OR P 180 }} i dTQP2 { 1 2 } {{ P OR P OR 180 }} i dTQP2 { 2 3 } {{ OP2 P OR P 60 }} i dTQP2 { 2 3 } {{ P OR P OR 180 }} i dTQP2 { 3 4 } {{ OP2 P OR P 60 }} i dTQP2 { 3 4 } {{ P OR P OR 180 }} i dTQP2 { 4 5 } {{ OP2 P OR C5' 60 }} i UQP2 { 1 2 } {{ OP1 P OR P 180 }} i UQP2 { 1 2 } {{ P OR P OR 180 }} i UQP2 { 2 3 } {{ OP2 P OR P 60 }} i UQP2 { 2 3 } {{ P OR P OR 180 }} i UQP2 { 3 4 } {{ OP2 P OR P 60 }} i UQP2 { 3 4 } {{ P OR P OR 180 }} i UQP2 { 4 5 } {{ OP2 P OR C5' 60 }} # Just examples for checking gometries... # or use the command "savemol2 unit unit.mol2 0" & read the dihedral values using VMD... mg ADP1.1.OH ADP1.1.P ADP1.1.OR ADP1.2.P mg ADP1.1.P ADP1.1.OR ADP1.2.P ADP1.2.OR mg ADP1.1.OR ADP1.2.P ADP1.2.OR ADP1.3.C5' mg ATP1.1.OH ATP1.1.P ATP1.1.OR ATP1.2.P mg ATP1.1.P ATP1.1.OR ATP1.2.P ATP1.2.OR mg ATP1.1.OR ATP1.2.P ATP1.2.OR ATP1.3.P mg ATP1.2.P ATP1.2.OR ATP1.3.P ATP1.3.OR mg ATP1.2.OR ATP1.3.P ATP1.3.OR ATP1.4.C5' mg ADP2.1.OP1 ADP2.1.P ADP2.1.OR ADP2.2.P mg ADP2.1.P ADP2.1.OR ADP2.2.P ADP2.2.OR mg ADP2.1.OR ADP2.2.P ADP2.2.OR ADP2.3.C5' mg ATP2.1.OP1 ATP2.1.P ATP2.1.OR ATP2.2.P mg ATP2.1.P ATP2.1.OR ATP2.2.P ATP2.2.OR mg ATP2.1.OR ATP2.2.P ATP2.2.OR ATP2.3.P mg ATP2.2.P ATP2.2.OR ATP2.3.P ATP2.3.OR mg ATP2.2.OR ATP2.3.P ATP2.3.OR ATP2.4.C5' # Set the name of each library individually before saving it in the global library set dAMP1 name "dAMP1" set dAMP2 name "dAMP2" set dADP1 name "dADP1" set dADP2 name "dADP2" set dATP1 name "dATP1" set dATP2 name "dATP2" set dAQP1 name "dAQP1" set dAQP2 name "dAQP2" set dCMP1 name "dCMP1" set dCMP2 name "dCMP2" set dCDP1 name "dCDP1" set dCDP2 name "dCDP2" set dCTP1 name "dCTP1" set dCTP2 name "dCTP2" set dCQP1 name "dCQP1" set dCQP2 name "dCQP2" set dGMP1 name "dGMP1" set dGMP2 name "dGMP2" set dGDP1 name "dGDP1" set dGDP2 name "dGDP2" set dGTP1 name "dGTP1" set dGTP2 name "dGTP2" set dGQP1 name "dGQP1" set dGQP2 name "dGQP2" set dTMP1 name "dTMP1" set dTMP2 name "dTMP2" set dTDP1 name "dTDP1" set dTDP2 name "dTDP2" set dTTP1 name "dTTP1" set dTTP2 name "dTTP2" set dTQP1 name "dTQP1" set dTQP2 name "dTQP2" set AMP1 name "AMP1" set AMP2 name "AMP2" set ADP1 name "ADP1" set ADP2 name "ADP2" set ATP1 name "ATP1" set ATP2 name "ATP2" set AQP1 name "AQP1" set AQP2 name "AQP2" set CMP1 name "CMP1" set CMP2 name "CMP2" set CDP1 name "CDP1" set CDP2 name "CDP2" set CTP1 name "CTP1" set CTP2 name "CTP2" set CQP1 name "CQP1" set CQP2 name "CQP2" set GMP1 name "GMP1" set GMP2 name "GMP2" set GDP1 name "GDP1" set GDP2 name "GDP2" set GTP1 name "GTP1" set GTP2 name "GTP2" set GQP1 name "GQP1" set GQP2 name "GQP2" set UMP1 name "UMP1" set UMP2 name "UMP2" set UDP1 name "UDP1" set UDP2 name "UDP2" set UTP1 name "UTP1" set UTP2 name "UTP2" set UQP1 name "UQP1" set UQP2 name "UQP2" # Individually save each OFF library in the global library q4md-forcefieldtools-cofactors.off saveoff dAMP1 q4md-forcefieldtools-cofactors.off saveoff dAMP2 q4md-forcefieldtools-cofactors.off saveoff dADP1 q4md-forcefieldtools-cofactors.off saveoff dADP2 q4md-forcefieldtools-cofactors.off saveoff dATP1 q4md-forcefieldtools-cofactors.off saveoff dATP2 q4md-forcefieldtools-cofactors.off saveoff dAQP1 q4md-forcefieldtools-cofactors.off saveoff dAQP2 q4md-forcefieldtools-cofactors.off saveoff dCMP1 q4md-forcefieldtools-cofactors.off saveoff dCMP2 q4md-forcefieldtools-cofactors.off saveoff dCDP1 q4md-forcefieldtools-cofactors.off saveoff dCDP2 q4md-forcefieldtools-cofactors.off saveoff dCTP1 q4md-forcefieldtools-cofactors.off saveoff dCTP2 q4md-forcefieldtools-cofactors.off saveoff dCQP1 q4md-forcefieldtools-cofactors.off saveoff dCQP2 q4md-forcefieldtools-cofactors.off saveoff dGMP1 q4md-forcefieldtools-cofactors.off saveoff dGMP2 q4md-forcefieldtools-cofactors.off saveoff dGDP1 q4md-forcefieldtools-cofactors.off saveoff dGDP2 q4md-forcefieldtools-cofactors.off saveoff dGTP1 q4md-forcefieldtools-cofactors.off saveoff dGTP2 q4md-forcefieldtools-cofactors.off saveoff dGQP1 q4md-forcefieldtools-cofactors.off saveoff dGQP2 q4md-forcefieldtools-cofactors.off saveoff dTMP1 q4md-forcefieldtools-cofactors.off saveoff dTMP2 q4md-forcefieldtools-cofactors.off saveoff dTDP1 q4md-forcefieldtools-cofactors.off saveoff dTDP2 q4md-forcefieldtools-cofactors.off saveoff dTTP1 q4md-forcefieldtools-cofactors.off saveoff dTTP2 q4md-forcefieldtools-cofactors.off saveoff dTQP1 q4md-forcefieldtools-cofactors.off saveoff dTQP2 q4md-forcefieldtools-cofactors.off saveoff AMP1 q4md-forcefieldtools-cofactors.off saveoff AMP2 q4md-forcefieldtools-cofactors.off saveoff ADP1 q4md-forcefieldtools-cofactors.off saveoff ADP2 q4md-forcefieldtools-cofactors.off saveoff ATP1 q4md-forcefieldtools-cofactors.off saveoff ATP2 q4md-forcefieldtools-cofactors.off saveoff AQP1 q4md-forcefieldtools-cofactors.off saveoff AQP2 q4md-forcefieldtools-cofactors.off saveoff CMP1 q4md-forcefieldtools-cofactors.off saveoff CMP2 q4md-forcefieldtools-cofactors.off saveoff CDP1 q4md-forcefieldtools-cofactors.off saveoff CDP2 q4md-forcefieldtools-cofactors.off saveoff CTP1 q4md-forcefieldtools-cofactors.off saveoff CTP2 q4md-forcefieldtools-cofactors.off saveoff CQP1 q4md-forcefieldtools-cofactors.off saveoff CQP2 q4md-forcefieldtools-cofactors.off saveoff GMP1 q4md-forcefieldtools-cofactors.off saveoff GMP2 q4md-forcefieldtools-cofactors.off saveoff GDP1 q4md-forcefieldtools-cofactors.off saveoff GDP2 q4md-forcefieldtools-cofactors.off saveoff GTP1 q4md-forcefieldtools-cofactors.off saveoff GTP2 q4md-forcefieldtools-cofactors.off saveoff GQP1 q4md-forcefieldtools-cofactors.off saveoff GQP2 q4md-forcefieldtools-cofactors.off saveoff UMP1 q4md-forcefieldtools-cofactors.off saveoff UMP2 q4md-forcefieldtools-cofactors.off saveoff UDP1 q4md-forcefieldtools-cofactors.off saveoff UDP2 q4md-forcefieldtools-cofactors.off saveoff UTP1 q4md-forcefieldtools-cofactors.off saveoff UTP2 q4md-forcefieldtools-cofactors.off saveoff UQP1 q4md-forcefieldtools-cofactors.off saveoff UQP2 q4md-forcefieldtools-cofactors.off # Individually save each library in the tripos mol2 file format for structure visualization into VMD # See http://upjv.q4md-forcefieldtools.org/Tutorial/leap.php or use Amber 10 savemol2 dAMP1 dAMP1.mol2 0 savemol2 dAMP2 dAMP2.mol2 0 savemol2 dADP1 dADP1.mol2 0 savemol2 dADP2 dADP2.mol2 0 savemol2 dATP1 dATP1.mol2 0 savemol2 dATP2 dATP2.mol2 0 savemol2 dAQP1 dAQP1.mol2 0 savemol2 dAQP2 dAQP2.mol2 0 savemol2 dCMP1 dCMP1.mol2 0 savemol2 dCMP2 dCMP2.mol2 0 savemol2 dCDP1 dCDP1.mol2 0 savemol2 dCDP2 dCDP2.mol2 0 savemol2 dCTP1 dCTP1.mol2 0 savemol2 dCTP2 dCTP2.mol2 0 savemol2 dCQP1 dCQP1.mol2 0 savemol2 dCQP2 dCQP2.mol2 0 savemol2 dGMP1 dGMP1.mol2 0 savemol2 dGMP2 dGMP2.mol2 0 savemol2 dGDP1 dGDP1.mol2 0 savemol2 dGDP2 dGDP2.mol2 0 savemol2 dGTP1 dGTP1.mol2 0 savemol2 dGTP2 dGTP2.mol2 0 savemol2 dGQP1 dGQP1.mol2 0 savemol2 dGQP2 dGQP2.mol2 0 savemol2 dTMP1 dTMP1.mol2 0 savemol2 dTMP2 dTMP2.mol2 0 savemol2 dTDP1 dTDP1.mol2 0 savemol2 dTDP2 dTDP2.mol2 0 savemol2 dTTP1 dTTP1.mol2 0 savemol2 dTTP2 dTTP2.mol2 0 savemol2 dTQP1 dTQP1.mol2 0 savemol2 dTQP2 dTQP2.mol2 0 savemol2 AMP1 AMP1.mol2 0 savemol2 AMP2 AMP2.mol2 0 savemol2 ADP1 ADP1.mol2 0 savemol2 ADP2 ADP2.mol2 0 savemol2 ATP1 ATP1.mol2 0 savemol2 ATP2 ATP2.mol2 0 savemol2 AQP1 AQP1.mol2 0 savemol2 AQP2 AQP2.mol2 0 savemol2 CMP1 CMP1.mol2 0 savemol2 CMP2 CMP2.mol2 0 savemol2 CDP1 CDP1.mol2 0 savemol2 CDP2 CDP2.mol2 0 savemol2 CTP1 CTP1.mol2 0 savemol2 CTP2 CTP2.mol2 0 savemol2 CQP1 CQP1.mol2 0 savemol2 CQP2 CQP2.mol2 0 savemol2 GMP1 GMP1.mol2 0 savemol2 GMP2 GMP2.mol2 0 savemol2 GDP1 GDP1.mol2 0 savemol2 GDP2 GDP2.mol2 0 savemol2 GTP1 GTP1.mol2 0 savemol2 GTP2 GTP2.mol2 0 savemol2 GQP1 GQP1.mol2 0 savemol2 GQP2 GQP2.mol2 0 savemol2 UMP1 UMP1.mol2 0 savemol2 UMP2 UMP2.mol2 0 savemol2 UDP1 UDP1.mol2 0 savemol2 UDP2 UDP2.mol2 0 savemol2 UTP1 UTP1.mol2 0 savemol2 UTP2 UTP2.mol2 0 savemol2 UQP1 UQP1.mol2 0 savemol2 UQP2 UQP2.mol2 0 # Above only connections between the 5' ribose position and the "phosphate system" were presented as examples. # However by analogy, one can easily generate connection(s) to the 5' position and/or the 3' position and/or the 2' position # AM3P1 = seq {P1M B3} # AM3P2 = seq {P2M B3} # AD3P1 = seq {P1M P1 B3} # AD3P2 = seq {P2M P1 B3} # AT3P1 = seq {P1M P1 P1 B3} # AT3P2 = seq {P2M P1 P1 B3} # AQ3P1 = seq {P1M P1 P1 P1 B3} # AQ3P2 = seq {P2M P1 P1 P1 B3} # # set AM3P1 name "AM3P1" # saveoff AM3P1 q4md-forcefieldtools-cofactors.off # savemol2 AM3P1 AM3P1.mol2 0 # # set AM3P2 name "AM3P2" # saveoff AM3P2 q4md-forcefieldtools-cofactors.off # savemol2 AM3P2 AM3P2.mol2 0 # # set AD3P1 name "AD3P1" # saveoff AD3P1 q4md-forcefieldtools-cofactors.off # savemol2 AD3P1 AD3P1.mol2 0 # # set AD3P2 name "AD3P2" # saveoff AD3P2 q4md-forcefieldtools-cofactors.off # savemol2 AD3P2 AD3P2.mol2 0 # # set AT3P1 name "AT3P1" # saveoff AT3P1 q4md-forcefieldtools-cofactors.off # savemol2 AT3P1 AT3P1.mol2 0 # # set AT3P2 name "AT3P2" # saveoff AT3P2 q4md-forcefieldtools-cofactors.off # savemol2 AT3P2 AT3P2.mol2 0 # # set AQ3P1 name "AQ3P1" # saveoff AQ3P1 q4md-forcefieldtools-cofactors.off # savemol2 AQ3P1 AQ3P1.mol2 0 # # set AQ3P2 name "AQ3P2" # saveoff AQ3P2 q4md-forcefieldtools-cofactors.off # savemol2 AQ3P2 AQ3P2.mol2 0 # # AM2P1 = seq {P1M B2} # AM2P2 = seq {P2M B2} # AD2P1 = seq {P1M P1 B2} # AD2P2 = seq {P2M P1 B2} # AT2P1 = seq {P1M P1 P1 B2} # AT2P2 = seq {P2M P1 P1 B2} # AQ2P1 = seq {P1M P1 P1 P1 B2} # AQ2P2 = seq {P2M P1 P1 P1 B2} # # Now let's demonstrate connections between the 5' & 3' ribose positions and two "phosphate systems" # TMP1 = seq {P1M B53} # set P1M head P1M.1.OR # set P2M head P2M.1.OR # EXAMPLE1 = seq {TMP1 P1M} # EXAMPLE2 = seq {TMP1 P2M} # # set EXAMPLE1 name "EXAMPLE1" # set EXAMPLE2 name "EXAMPLE2" # saveoff EXAMPLE1 q4md-forcefieldtools-cofactors.off # savemol2 EXAMPLE1 EXAMPLE1.mol2 0 # saveoff EXAMPLE2 q4md-forcefieldtools-cofactors.off # savemol2 EXAMPLE2 EXAMPLE2.mol2 0 # # TMP2 = seq {P1M P1 B53} # set P1M head P1M.1.OR # set P2M head P2M.1.OR # set P1 head P1.1.OR # set P1 tail P1.1.P # EXAMPLE3 = seq {TMP2 P1 P2M} # # set EXAMPLE3 name "EXAMPLE3" # saveoff EXAMPLE3 q4md-forcefieldtools-cofactors.off # savemol2 EXAMPLE3 EXAMPLE3.mol2 0 # etc... # 2) Let's continue with NXD, NXDH, NXDP, NXDPH X = dA, dC, dG, dT, A, C, G or U... # - The diphosphate POP unit has to be set between A, C, G, T, B, D, H or U and I or R # - a P1M (-1) or P2M (-2) terminal phosphate group might be added to the 3' and/or 2' ribose position of A, C, G, T, B, D, H or U and I or R # - as many as P1 central phosphate groups might be added between the terminal phosphate group and the selected ribose position set A5 tail A5.1.C5' set C5 tail C5.1.C5' set G5 tail G5.1.C5' set T5 tail T5.1.C5' dNAD = seq {A5 POP I5} dNADH = seq {A5 POP R5} dNCD = seq {C5 POP I5} dNCDH = seq {C5 POP R5} dNGD = seq {G5 POP I5} dNGDH = seq {G5 POP R5} dNTD = seq {T5 POP I5} dNTDH = seq {T5 POP R5} set B5 tail B5.1.C5' set D5 tail D5.1.C5' set H5 tail H5.1.C5' set U5 tail U5.1.C5' NAD = seq {B5 POP I5} NADH = seq {B5 POP R5} NCD = seq {D5 POP I5} NCDH = seq {D5 POP R5} NGD = seq {H5 POP I5} NGDH = seq {H5 POP R5} NUD = seq {U5 POP I5} NUDH = seq {U5 POP R5} # Adapt the geometries... # Just change the dihedral values if you want to set up a different conformation i dNAD { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i dNADH { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i dNCD { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i dNCDH { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i dNGD { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i dNGDH { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i dNTD { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i dNTDH { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NAD { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NADH { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NCD { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NCDH { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NGD { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NGDH { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NUD { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NUDH { 1 2 3 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} set B52 tail B52.1.C5' set B52 head B52.1.C2' set D52 tail D52.1.C5' set D52 head D52.1.C2' set H52 tail H52.1.C5' set H52 head H52.1.C2' set U52 tail U52.1.C5' set U52 head U52.1.C2' NADP1 = seq {P1M B52 POP I5} NCDP1 = seq {P1M D52 POP I5} NGDP1 = seq {P1M H52 POP I5} NUDP1 = seq {P1M U52 POP I5} NADP2 = seq {P2M B52 POP I5} NCDP2 = seq {P2M D52 POP I5} NGDP2 = seq {P2M H52 POP I5} NUDP2 = seq {P2M U52 POP I5} NADP1H = seq {P1M B52 POP R5} NCDP1H = seq {P1M D52 POP R5} NGDP1H = seq {P1M H52 POP R5} NUDP1H = seq {P1M U52 POP R5} NADP2H = seq {P2M B52 POP R5} NCDP2H = seq {P2M D52 POP R5} NGDP2H = seq {P2M H52 POP R5} NUDP2H = seq {P2M U52 POP R5} # Adapt the geometries... # Just change the dihedral values if you want to set up a different conformation i NADP1 { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NCDP1 { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NGDP1 { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NUDP1 { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NADP2 { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NCDP2 { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NGDP2 { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NUDP2 { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NADP1H { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NCDP1H { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NGDP1H { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NUDP1H { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NADP2H { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NCDP2H { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NGDP2H { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} i NUDP2H { 2 3 4 } {{ C5' O5A PA OP -80.0 }{ C5' O5B PB OP -80.0 }{ O5B PB OP PA 80.0 }{ PB OP PA O5A 80.0 }} set dNAD name "dNAD" set dNADH name "dNADH" set dNCD name "dNCD" set dNCDH name "dNCDH" set dNGD name "dNGD" set dNGDH name "dNGDH" set dNTD name "dNTD" set dNTDH name "dNTDH" set NAD name "NAD" set NADH name "NADH" set NCD name "NCD" set NCDH name "NCDH" set NGD name "NGD" set NGDH name "NGDH" set NUD name "NUD" set NUDH name "NUDH" set NADP1 name "NADP1" set NCDP1 name "NCDP1" set NGDP1 name "NGDP1" set NUDP1 name "NUDP1" set NADP2 name "NADP2" set NCDP2 name "NCDP2" set NGDP2 name "NGDP2" set NUDP2 name "NUDP2" set NADP1H name "NADP1H" set NCDP1H name "NCDP1H" set NGDP1H name "NGDP1H" set NUDP1H name "NUDP1H" set NADP2H name "NADP2H" set NCDP2H name "NCDP2H" set NGDP2H name "NGDP2H" set NUDP2H name "NUDP2H" saveoff dNAD q4md-forcefieldtools-cofactors.off saveoff dNADH q4md-forcefieldtools-cofactors.off saveoff dNCD q4md-forcefieldtools-cofactors.off saveoff dNCDH q4md-forcefieldtools-cofactors.off saveoff dNGD q4md-forcefieldtools-cofactors.off saveoff dNGDH q4md-forcefieldtools-cofactors.off saveoff dNTD q4md-forcefieldtools-cofactors.off saveoff dNTDH q4md-forcefieldtools-cofactors.off saveoff NAD q4md-forcefieldtools-cofactors.off saveoff NADH q4md-forcefieldtools-cofactors.off saveoff NCD q4md-forcefieldtools-cofactors.off saveoff NCDH q4md-forcefieldtools-cofactors.off saveoff NGD q4md-forcefieldtools-cofactors.off saveoff NGDH q4md-forcefieldtools-cofactors.off saveoff NUD q4md-forcefieldtools-cofactors.off saveoff NUDH q4md-forcefieldtools-cofactors.off saveoff NADP1 q4md-forcefieldtools-cofactors.off saveoff NCDP1 q4md-forcefieldtools-cofactors.off saveoff NGDP1 q4md-forcefieldtools-cofactors.off saveoff NUDP1 q4md-forcefieldtools-cofactors.off saveoff NADP2 q4md-forcefieldtools-cofactors.off saveoff NCDP2 q4md-forcefieldtools-cofactors.off saveoff NGDP2 q4md-forcefieldtools-cofactors.off saveoff NUDP2 q4md-forcefieldtools-cofactors.off saveoff NADP1H q4md-forcefieldtools-cofactors.off saveoff NCDP1H q4md-forcefieldtools-cofactors.off saveoff NGDP1H q4md-forcefieldtools-cofactors.off saveoff NUDP1H q4md-forcefieldtools-cofactors.off saveoff NADP2H q4md-forcefieldtools-cofactors.off saveoff NCDP2H q4md-forcefieldtools-cofactors.off saveoff NGDP2H q4md-forcefieldtools-cofactors.off saveoff NUDP2H q4md-forcefieldtools-cofactors.off # http://upjv.q4md-forcefieldtools.org/Tutorial/leap.php savemol2 dNAD dNAD.mol2 0 savemol2 dNADH dNADH.mol2 0 savemol2 dNCD dNCD.mol2 0 savemol2 dNCDH dNCDH.mol2 0 savemol2 dNGD dNGD.mol2 0 savemol2 dNGDH dNGDH.mol2 0 savemol2 dNTD dNTD.mol2 0 savemol2 dNTDH dNTDH.mol2 0 savemol2 NAD NAD.mol2 0 savemol2 NADH NADH.mol2 0 savemol2 NCD NCD.mol2 0 savemol2 NCDH NCDH.mol2 0 savemol2 NGD NGD.mol2 0 savemol2 NGDH NGDH.mol2 0 savemol2 NUD NUD.mol2 0 savemol2 NUDH NUDH.mol2 0 savemol2 NADP1 NADP1.mol2 0 savemol2 NCDP1 NCDP1.mol2 0 savemol2 NGDP1 NGDP1.mol2 0 savemol2 NUDP1 NUDP1.mol2 0 savemol2 NADP2 NADP2.mol2 0 savemol2 NCDP2 NCDP2.mol2 0 savemol2 NGDP2 NGDP2.mol2 0 savemol2 NUDP2 NUDP2.mol2 0 savemol2 NADP1H NADP1H.mol2 0 savemol2 NCDP1H NCDP1H.mol2 0 savemol2 NGDP1H NGDP1H.mol2 0 savemol2 NUDP1H NUDP1H.mol2 0 savemol2 NADP2H NADP2H.mol2 0 savemol2 NCDP2H NCDP2H.mol2 0 savemol2 NGDP2H NGDP2H.mol2 0 savemol2 NUDP2H NUDP2H.mol2 0 # - One can replace the XYZ unit (for instance B52) by one of the following ones: # X = A, C, G, U, I or R # - if Y = 5, Z = 3 or 2 # - if Y = 3, Z = 2 # - One can also replace the XYZ unit by a XN unit (see the whole list at the beginning of this file) # In this case a phosphate group will be added at the positions 3' and 2' of ribose. # # - Examples: similar derivatives but phosphate at position 3' instead of position 2' # set B53 tail B53.1.C5' # set B53 head B53.1.C3' # set D53 tail D53.1.C5' # set D53 head D53.1.C3' # set H53 tail H53.1.C5' # set H53 head H53.1.C3' # set U53 tail U53.1.C5' # set U53 head U53.1.C3' # NADP3 = seq {P1M B53 POP I5} # NCDP3 = seq {P1M D53 POP I5} # NGDP3 = seq {P1M H53 POP I5} # NUDP3 = seq {P1M U53 POP I5} # NADP4 = seq {P2M B53 POP I5} # NCDP4 = seq {P2M D53 POP I5} # NGDP4 = seq {P2M H53 POP I5} # NUDP4 = seq {P2M U53 POP I5} # NADP3H = seq {P1M B53 POP R5} # NCDP3H = seq {P1M D53 POP R5} # NGDP3H = seq {P1M H53 POP R5} # NUDP3H = seq {P1M U53 POP R5} # NADP4H = seq {P2M B53 POP R5} # NCDP4H = seq {P2M D53 POP R5} # NGDP4H = seq {P2M H53 POP R5} # NUDP4H = seq {P2M U53 POP R5} # 3) Let's continue with riboflavin, FMN, FXD and FXDH2 cofactors (X = dA, dC, dG, dT, A, C, G or U) # - The diphosphate POP unit is set between A, C, G, T, B, D, H or U and FLO or FLR # - a P1M (-1) or P2M (-2) terminal phosphate group might be added to the 3' and/or 2' ribose position of A, C, G, T, B, D, H or U or to the primary alcohol of riboflavin # - as many as P1 central phosphate groups might be added between the terminal phosphate group and the selected ribose position RBFLV = seq {LNO FLO} RBFLVH = seq {LNO FLR} FMN1 = seq {P1M LNK FLO} FMN1H = seq {P1M LNK FLR} FMN2 = seq {P2M LNK FLO} FMN2H = seq {P2M LNK FLR} # Adapt the geometries... # Just change the dihedral values if you want to set up a different conformation i RBFLV { 1 2 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i RBFLVH { 1 2 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i FMN1 { 1 2 } {{ "OH" "P" "OR" "C5" 180.0 }{ "P" "OR" "C5" "C4" 180.0 }{ "OR" "C5" "C4" "C3" 180.0 }} i FMN1 { 2 3 } {{"C2" "C1" "N10" "C9A" 90.0 }} i FMN1H { 1 2 } {{ "OH" "P" "OR" "C5" 180.0 }{ "P" "OR" "C5" "C4" 180.0 }{ "OR" "C5" "C4" "C3" 180.0 }} i FMN1H { 2 3 } {{"C2" "C1" "N10" "C9A" 120.0 }} i FMN2 { 1 2 } {{ "P" "OR" "C5" "C4" 180.0 }{ "OR" "C5" "C4" "C3" 180.0 }} i FMN2 { 2 3 } {{"C2" "C1" "N10" "C9A" 90.0 }} i FMN2H { 1 2 } {{ "P" "OR" "C5" "C4" 180.0 }{ "OR" "C5" "C4" "C3" 180.0 }} i FMN2H { 2 3 } {{"C2" "C1" "N10" "C9A" 120.0 }} set RBFLV name "RBFLV" set RBFLVH name "RBFLVH" set FMN1 name "FMN1" set FMN1H name "FMN1H" set FMN2 name "FMN2" set FMN2H name "FMN2H" saveoff RBFLV q4md-forcefieldtools-cofactors.off saveoff RBFLVH q4md-forcefieldtools-cofactors.off saveoff FMN1 q4md-forcefieldtools-cofactors.off saveoff FMN1H q4md-forcefieldtools-cofactors.off saveoff FMN2 q4md-forcefieldtools-cofactors.off saveoff FMN2H q4md-forcefieldtools-cofactors.off # http://upjv.q4md-forcefieldtools.org/Tutorial/leap.php savemol2 RBFLV RBFLV.mol2 0 savemol2 RBFLVH RBFLVH.mol2 0 savemol2 FMN1 FMN1.mol2 0 savemol2 FMN1H FMN1H.mol2 0 savemol2 FMN2 FMN2.mol2 0 savemol2 FMN2H FMN2H.mol2 0 set A5 tail A5.1.C5' set C5 tail C5.1.C5' set G5 tail G5.1.C5' set T5 tail T5.1.C5' dFAD = seq {A5 POP LNK FLO} dFADH = seq {A5 POP LNK FLR} dFCD = seq {C5 POP LNK FLO} dFCDH = seq {C5 POP LNK FLR} dFGD = seq {G5 POP LNK FLO} dFGDH = seq {G5 POP LNK FLR} dFUD = seq {T5 POP LNK FLO} dFUDH = seq {T5 POP LNK FLR} set B5 tail B5.1.C5' set D5 tail D5.1.C5' set H5 tail H5.1.C5' set U5 tail U5.1.C5' FAD = seq {B5 POP LNK FLO} FADH = seq {B5 POP LNK FLR} FCD = seq {D5 POP LNK FLO} FCDH = seq {D5 POP LNK FLR} FGD = seq {H5 POP LNK FLO} FGDH = seq {H5 POP LNK FLR} FUD = seq {U5 POP LNK FLO} FUDH = seq {U5 POP LNK FLR} i dFAD { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dFAD { 3 4 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i dFADH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dFADH { 3 4 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i dFCD { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dFCD { 3 4 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i dFCDH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dFCDH { 3 4 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i dFGD { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dFGD { 3 4 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i dFGDH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dFGDH { 3 4 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i dFUD { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dFUD { 3 4 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i dFUDH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dFUDH { 3 4 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i FAD { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FAD { 3 4 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i FADH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FADH { 3 4 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i FCD { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FCD { 3 4 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i FCDH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FCDH { 3 4 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i FGD { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FGD { 3 4 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i FGDH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FGDH { 3 4 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i FUD { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FUD { 3 4 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i FUDH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FUDH { 3 4 } {{ "C2" "C1" "N10" "C9A" 120.0 }} set dFAD name "dFAD" set dFADH name "dFADH" set dFCD name "dFCD" set dFCDH name "dFCDH" set dFGD name "dFGD" set dFGDH name "dFGDH" set dFUD name "dFUD" set dFUDH name "dFUDH" set FAD name "FAD" set FADH name "FADH" set FCD name "FCD" set FCDH name "FCDH" set FGD name "FGD" set FGDH name "FGDH" set FUD name "FUD" set FUDH name "FUDH" saveoff dFAD q4md-forcefieldtools-cofactors.off saveoff dFADH q4md-forcefieldtools-cofactors.off saveoff dFCD q4md-forcefieldtools-cofactors.off saveoff dFCDH q4md-forcefieldtools-cofactors.off saveoff dFGD q4md-forcefieldtools-cofactors.off saveoff dFGDH q4md-forcefieldtools-cofactors.off saveoff dFUD q4md-forcefieldtools-cofactors.off saveoff dFUDH q4md-forcefieldtools-cofactors.off saveoff FAD q4md-forcefieldtools-cofactors.off saveoff FADH q4md-forcefieldtools-cofactors.off saveoff FCD q4md-forcefieldtools-cofactors.off saveoff FCDH q4md-forcefieldtools-cofactors.off saveoff FGD q4md-forcefieldtools-cofactors.off saveoff FGDH q4md-forcefieldtools-cofactors.off saveoff FUD q4md-forcefieldtools-cofactors.off saveoff FUDH q4md-forcefieldtools-cofactors.off # http://upjv.q4md-forcefieldtools.org/Tutorial/leap.php savemol2 dFAD dFAD.mol2 0 savemol2 dFADH dFADH.mol2 0 savemol2 dFCD dFCD.mol2 0 savemol2 dFCDH dFCDH.mol2 0 savemol2 dFGD dFGD.mol2 0 savemol2 dFGDH dFGDH.mol2 0 savemol2 dFUD dFUD.mol2 0 savemol2 dFUDH dFUDH.mol2 0 savemol2 FAD FAD.mol2 0 savemol2 FADH FADH.mol2 0 savemol2 FCD FCD.mol2 0 savemol2 FCDH FCDH.mol2 0 savemol2 FGD FGD.mol2 0 savemol2 FGDH FGDH.mol2 0 savemol2 FUD FUD.mol2 0 savemol2 FUDH FUDH.mol2 0 set B52 tail B52.1.C5' set B52 head B52.1.C2' set D52 tail D52.1.C5' set D52 head D52.1.C2' set H52 tail H52.1.C5' set H52 head H52.1.C2' set U52 tail U52.1.C5' set U52 head U52.1.C2' FADP1 = seq {P1M B52 POP LNK FLO} FADHP1 = seq {P1M B52 POP LNK FLR} FCDP1 = seq {P1M D52 POP LNK FLO} FCDHP1 = seq {P1M D52 POP LNK FLR} FGDP1 = seq {P1M H52 POP LNK FLO} FGDHP1 = seq {P1M H52 POP LNK FLR} FUDP1 = seq {P1M U52 POP LNK FLO} FUDHP1 = seq {P1M U52 POP LNK FLR} FADP2 = seq {P2M B52 POP LNK FLO} FADHP2 = seq {P2M B52 POP LNK FLR} FCDP2 = seq {P2M D52 POP LNK FLO} FCDHP2 = seq {P2M D52 POP LNK FLR} FGDP2 = seq {P2M H52 POP LNK FLO} FGDHP2 = seq {P2M H52 POP LNK FLR} FUDP2 = seq {P2M U52 POP LNK FLO} FUDHP2 = seq {P2M U52 POP LNK FLR} i FADP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FADP1 { 4 5 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i FADHP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FADHP1 { 4 5 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i FCDP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FCDP1 { 4 5 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i FCDHP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FCDHP1 { 4 5 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i FGDP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FGDP1 { 4 5 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i FGDHP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FGDHP1 { 4 5 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i FUDP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FUDP1 { 4 5 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i FUDHP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FUDHP1 { 4 5 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i FADP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FADP2 { 4 5 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i FADHP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FADHP2 { 4 5 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i FCDP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FCDP2 { 4 5 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i FCDHP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FCDHP2 { 4 5 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i FGDP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FGDP2 { 4 5 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i FGDHP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FGDHP2 { 4 5 } {{ "C2" "C1" "N10" "C9A" 120.0 }} i FUDP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FUDP2 { 4 5 } {{ "C2" "C1" "N10" "C9A" 90.0 }} i FUDHP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C5" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i FUDHP2 { 4 5 } {{ "C2" "C1" "N10" "C9A" 120.0 }} set FADP1 name "FADP1" set FADHP1 name "FADHP1" set FCDP1 name "FCDP1" set FCDHP1 name "FCDHP1" set FGDP1 name "FGDP1" set FGDHP1 name "FGDHP1" set FUDP1 name "FUDP1" set FUDHP1 name "FUDHP1" set FADP2 name "FADP2" set FADHP2 name "FADHP2" set FCDP2 name "FCDP2" set FCDHP2 name "FCDHP2" set FGDP2 name "FGDP2" set FGDHP2 name "FGDHP2" set FUDP2 name "FUDP2" set FUDHP2 name "FUDHP2" saveoff FADP1 q4md-forcefieldtools-cofactors.off saveoff FADHP1 q4md-forcefieldtools-cofactors.off saveoff FCDP1 q4md-forcefieldtools-cofactors.off saveoff FCDHP1 q4md-forcefieldtools-cofactors.off saveoff FGDP1 q4md-forcefieldtools-cofactors.off saveoff FGDHP1 q4md-forcefieldtools-cofactors.off saveoff FUDP1 q4md-forcefieldtools-cofactors.off saveoff FUDHP1 q4md-forcefieldtools-cofactors.off saveoff FADP2 q4md-forcefieldtools-cofactors.off saveoff FADHP2 q4md-forcefieldtools-cofactors.off saveoff FCDP2 q4md-forcefieldtools-cofactors.off saveoff FCDHP2 q4md-forcefieldtools-cofactors.off saveoff FGDP2 q4md-forcefieldtools-cofactors.off saveoff FGDHP2 q4md-forcefieldtools-cofactors.off saveoff FUDP2 q4md-forcefieldtools-cofactors.off saveoff FUDHP2 q4md-forcefieldtools-cofactors.off # http://upjv.q4md-forcefieldtools.org/Tutorial/leap.php savemol2 FADP1 FADP1.mol2 0 savemol2 FADHP1 FADHP1.mol2 0 savemol2 FCDP1 FCDP1.mol2 0 savemol2 FCDHP1 FCDHP1.mol2 0 savemol2 FGDP1 FGDP1.mol2 0 savemol2 FGDHP1 FGDHP1.mol2 0 savemol2 FUDP1 FUDP1.mol2 0 savemol2 FUDHP1 FUDHP1.mol2 0 savemol2 FADP2 FADP2.mol2 0 savemol2 FADHP2 FADHP2.mol2 0 savemol2 FCDP2 FCDP2.mol2 0 savemol2 FCDHP2 FCDHP2.mol2 0 savemol2 FGDP2 FGDP2.mol2 0 savemol2 FGDHP2 FGDHP2.mol2 0 savemol2 FUDP2 FUDP2.mol2 0 savemol2 FUDHP2 FUDHP2.mol2 0 # 4) Let's continue with Acetyl-coenzyme A, coenzyme A and even more # First, the fatty acid (S-acetylated or not; phosphorylated or not) ACOA = seq { AO1 AC2 AC3 } COA = seq { AO1 AC2 AC4 } ACOAP1 = seq { P1M AC1 AC2 AC3 } COAP1 = seq { P1M AC1 AC2 AC4 } ACOAP2 = seq { P2M AC1 AC2 AC3 } COAP2 = seq { P2M AC1 AC2 AC4 } set ACOA name "ACOA" set COA name "COA" set ACOAP1 name "ACOAP1" set COAP1 name "COAP1" set ACOAP2 name "ACOAP2" set COAP2 name "COAP2" saveoff ACOA q4md-forcefieldtools-cofactors.off saveoff COA q4md-forcefieldtools-cofactors.off saveoff ACOAP1 q4md-forcefieldtools-cofactors.off saveoff COAP1 q4md-forcefieldtools-cofactors.off saveoff ACOAP2 q4md-forcefieldtools-cofactors.off saveoff COAP2 q4md-forcefieldtools-cofactors.off # http://upjv.q4md-forcefieldtools.org/Tutorial/leap.php savemol2 ACOA ACOA.mol2 0 savemol2 COA COA.mol2 0 savemol2 ACOAP1 ACOAP1.mol2 0 savemol2 COAP1 COAP1.mol2 0 savemol2 ACOAP2 ACOAP2.mol2 0 savemol2 COAP2 COAP2.mol2 0 dCOASAC = seq {A5 POP AC1 AC2 AC3} dCOASH = seq {A5 POP AC1 AC2 AC4} dCOCSAC = seq {C5 POP AC1 AC2 AC3} dCOCSH = seq {C5 POP AC1 AC2 AC4} dCOGSAC = seq {G5 POP AC1 AC2 AC3} dCOGSH = seq {G5 POP AC1 AC2 AC4} dCOTSAC = seq {T5 POP AC1 AC2 AC3} dCOTSH = seq {T5 POP AC1 AC2 AC4} COASAC = seq {B5 POP AC1 AC2 AC3} COASH = seq {B5 POP AC1 AC2 AC4} COCSAC = seq {D5 POP AC1 AC2 AC3} COCSH = seq {D5 POP AC1 AC2 AC4} COGSAC = seq {H5 POP AC1 AC2 AC3} COGSH = seq {H5 POP AC1 AC2 AC4} COUSAC = seq {U5 POP AC1 AC2 AC3} COUSH = seq {U5 POP AC1 AC2 AC4} i dCOASH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOASAC { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOCSH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOCSAC { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOGSH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOGSAC { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOTSH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOTSAC { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COASH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COASAC { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COCSH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COCSAC { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COGSH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COGSAC { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COUSH { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COUSAC { 1 2 3 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} set dCOASH name "dCOASH" set dCOASAC name "dCOASAC" set dCOCSH name "dCOCSH" set dCOCSAC name "dCOCSAC" set dCOGSH name "dCOGSH" set dCOGSAC name "dCOGSAC" set dCOTSH name "dCOTSH" set dCOTSAC name "dCOTSAC" set COASH name "COASH" set COASAC name "COASAC" set COCSH name "COCSH" set COCSAC name "COCSAC" set COGSH name "COGSH" set COGSAC name "COGSAC" set COUSH name "COUSH" set COUSAC name "COUSAC" saveoff dCOASH q4md-forcefieldtools-cofactors.off saveoff dCOASAC q4md-forcefieldtools-cofactors.off saveoff dCOCSH q4md-forcefieldtools-cofactors.off saveoff dCOCSAC q4md-forcefieldtools-cofactors.off saveoff dCOGSH q4md-forcefieldtools-cofactors.off saveoff dCOGSAC q4md-forcefieldtools-cofactors.off saveoff dCOTSH q4md-forcefieldtools-cofactors.off saveoff dCOTSAC q4md-forcefieldtools-cofactors.off saveoff COASH q4md-forcefieldtools-cofactors.off saveoff COASAC q4md-forcefieldtools-cofactors.off saveoff COCSH q4md-forcefieldtools-cofactors.off saveoff COCSAC q4md-forcefieldtools-cofactors.off saveoff COGSH q4md-forcefieldtools-cofactors.off saveoff COGSAC q4md-forcefieldtools-cofactors.off saveoff COUSH q4md-forcefieldtools-cofactors.off saveoff COUSAC q4md-forcefieldtools-cofactors.off # http://upjv.q4md-forcefieldtools.org/Tutorial/leap.php savemol2 dCOASH dCOASH.mol2 0 savemol2 dCOASAC dCOASAC.mol2 0 savemol2 dCOCSH dCOCSH.mol2 0 savemol2 dCOCSAC dCOCSAC.mol2 0 savemol2 dCOGSH dCOGSH.mol2 0 savemol2 dCOGSAC dCOGSAC.mol2 0 savemol2 dCOTSH dCOTSH.mol2 0 savemol2 dCOTSAC dCOTSAC.mol2 0 savemol2 COASH COASH.mol2 0 savemol2 COASAC COASAC.mol2 0 savemol2 COCSH COCSH.mol2 0 savemol2 COCSAC COCSAC.mol2 0 savemol2 COGSH COGSH.mol2 0 savemol2 COGSAC COGSAC.mol2 0 savemol2 COUSH COUSH.mol2 0 savemol2 COUSAC COUSAC.mol2 0 set AC tail AC.1.C5' set AC head AC.1.C3' set CC tail CC.1.C5' set CC head CC.1.C3' set GC tail GC.1.C5' set GC head GC.1.C3' set TC tail TC.1.C5' set TC head TC.1.C3' set B53 tail B53.1.C5' set B53 head B53.1.C3' set D53 tail D53.1.C5' set D53 head D53.1.C3' set H53 tail H53.1.C5' set H53 head H53.1.C3' set U53 tail U53.1.C5' set U53 head U53.1.C3' dCOASACP1 = seq {P1M AC POP AC1 AC2 AC3} dCOASHP1 = seq {P1M AC POP AC1 AC2 AC4} dCOASACP2 = seq {P2M AC POP AC1 AC2 AC3} dCOASHP2 = seq {P2M AC POP AC1 AC2 AC4} dCOCSACP1 = seq {P1M CC POP AC1 AC2 AC3} dCOCSHP1 = seq {P1M CC POP AC1 AC2 AC4} dCOCSACP2 = seq {P2M CC POP AC1 AC2 AC3} dCOCSHP2 = seq {P2M CC POP AC1 AC2 AC4} dCOGSACP1 = seq {P1M GC POP AC1 AC2 AC3} dCOGSHP1 = seq {P1M GC POP AC1 AC2 AC4} dCOGSACP2 = seq {P2M GC POP AC1 AC2 AC3} dCOGSHP2 = seq {P2M GC POP AC1 AC2 AC4} dCOTSACP1 = seq {P1M TC POP AC1 AC2 AC3} dCOTSHP1 = seq {P1M TC POP AC1 AC2 AC4} dCOTSACP2 = seq {P2M TC POP AC1 AC2 AC3} dCOTSHP2 = seq {P2M TC POP AC1 AC2 AC4} COASACP1 = seq {P1M B53 POP AC1 AC2 AC3} COASHP1 = seq {P1M B53 POP AC1 AC2 AC4} COASACP2 = seq {P2M B53 POP AC1 AC2 AC3} COASHP2 = seq {P2M B53 POP AC1 AC2 AC4} COCSACP1 = seq {P1M D53 POP AC1 AC2 AC3} COCSHP1 = seq {P1M D53 POP AC1 AC2 AC4} COCSACP2 = seq {P2M D53 POP AC1 AC2 AC3} COCSHP2 = seq {P2M D53 POP AC1 AC2 AC4} COGSACP1 = seq {P1M H53 POP AC1 AC2 AC3} COGSHP1 = seq {P1M H53 POP AC1 AC2 AC4} COGSACP2 = seq {P2M H53 POP AC1 AC2 AC3} COGSHP2 = seq {P2M H53 POP AC1 AC2 AC4} COUSACP1 = seq {P1M U53 POP AC1 AC2 AC3} COUSHP1 = seq {P1M U53 POP AC1 AC2 AC4} COUSACP2 = seq {P2M U53 POP AC1 AC2 AC3} COUSHP2 = seq {P2M U53 POP AC1 AC2 AC4} i dCOASHP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOASACP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOASHP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOASACP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOCSHP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOCSACP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOCSHP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOCSACP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOGSHP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOGSACP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOGSHP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOGSACP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOTSHP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOTSACP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOTSHP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i dCOTSACP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COASHP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COASACP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COASHP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COASACP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COCSHP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COCSACP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COCSHP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COCSACP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COGSHP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COGSACP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COGSHP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COGSACP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COUSHP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COUSACP1 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COUSHP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} i COUSACP2 { 2 3 4 } {{ "C5'" "O5A" "PA" "OP" -80.0 }{ "C1" "O5B" "PB" "OP" -80.0 }{ "O5B" "PB" "OP" "PA" 80.0 }{ "PB" "OP" "PA" "O5A" 80.0 }} set dCOASHP1 name "COASHP1" set dCOASACP1 name "COASACP1" set dCOASHP2 name "COASHP2" set dCOASACP2 name "COASACP2" set dCOCSHP1 name "COCSHP1" set dCOCSACP1 name "COCSACP1" set dCOCSHP2 name "COCSHP2" set dCOCSACP2 name "COCSACP2" set dCOGSHP1 name "COGSHP1" set dCOGSACP1 name "COGSACP1" set dCOGSHP2 name "COGSHP2" set dCOGSACP2 name "COGSACP2" set dCOTSHP1 name "COTSHP1" set dCOTSACP1 name "COTSACP1" set dCOTSHP2 name "COTSHP2" set dCOTSACP2 name "COTSACP2" set COASHP1 name "COASHP1" set COASACP1 name "COASACP1" set COASHP2 name "COASHP2" set COASACP2 name "COASACP2" set COCSHP1 name "COCSHP1" set COCSACP1 name "COCSACP1" set COCSHP2 name "COCSHP2" set COCSACP2 name "COCSACP2" set COGSHP1 name "COGSHP1" set COGSACP1 name "COGSACP1" set COGSHP2 name "COGSHP2" set COGSACP2 name "COGSACP2" set COUSHP1 name "COUSHP1" set COUSACP1 name "COUSACP1" set COUSHP2 name "COUSHP2" set COUSACP2 name "COUSACP2" saveoff dCOASHP1 q4md-forcefieldtools-cofactors.off saveoff dCOASACP1 q4md-forcefieldtools-cofactors.off saveoff dCOASHP2 q4md-forcefieldtools-cofactors.off saveoff dCOASACP2 q4md-forcefieldtools-cofactors.off saveoff dCOCSHP1 q4md-forcefieldtools-cofactors.off saveoff dCOCSACP1 q4md-forcefieldtools-cofactors.off saveoff dCOCSHP2 q4md-forcefieldtools-cofactors.off saveoff dCOCSACP2 q4md-forcefieldtools-cofactors.off saveoff dCOGSHP1 q4md-forcefieldtools-cofactors.off saveoff dCOGSACP1 q4md-forcefieldtools-cofactors.off saveoff dCOGSHP2 q4md-forcefieldtools-cofactors.off saveoff dCOGSACP2 q4md-forcefieldtools-cofactors.off saveoff dCOTSHP1 q4md-forcefieldtools-cofactors.off saveoff dCOTSACP1 q4md-forcefieldtools-cofactors.off saveoff dCOTSHP2 q4md-forcefieldtools-cofactors.off saveoff dCOTSACP2 q4md-forcefieldtools-cofactors.off saveoff COASHP1 q4md-forcefieldtools-cofactors.off saveoff COASACP1 q4md-forcefieldtools-cofactors.off saveoff COASHP2 q4md-forcefieldtools-cofactors.off saveoff COASACP2 q4md-forcefieldtools-cofactors.off saveoff COCSHP1 q4md-forcefieldtools-cofactors.off saveoff COCSACP1 q4md-forcefieldtools-cofactors.off saveoff COCSHP2 q4md-forcefieldtools-cofactors.off saveoff COCSACP2 q4md-forcefieldtools-cofactors.off saveoff COGSHP1 q4md-forcefieldtools-cofactors.off saveoff COGSACP1 q4md-forcefieldtools-cofactors.off saveoff COGSHP2 q4md-forcefieldtools-cofactors.off saveoff COGSACP2 q4md-forcefieldtools-cofactors.off saveoff COUSHP1 q4md-forcefieldtools-cofactors.off saveoff COUSACP1 q4md-forcefieldtools-cofactors.off saveoff COUSHP2 q4md-forcefieldtools-cofactors.off saveoff COUSACP2 q4md-forcefieldtools-cofactors.off # http://upjv.q4md-forcefieldtools.org/Tutorial/leap.php savemol2 dCOASHP1 dCOASHP1.mol2 0 savemol2 dCOASACP1 dCOASACP1.mol2 0 savemol2 dCOASHP2 dCOASHP2.mol2 0 savemol2 dCOASACP2 dCOASACP2.mol2 0 savemol2 dCOCSHP1 dCOCSHP1.mol2 0 savemol2 dCOCSACP1 dCOCSACP1.mol2 0 savemol2 dCOCSHP2 dCOCSHP2.mol2 0 savemol2 dCOCSACP2 dCOCSACP2.mol2 0 savemol2 dCOGSHP1 dCOGSHP1.mol2 0 savemol2 dCOGSACP1 dCOGSACP1.mol2 0 savemol2 dCOGSHP2 dCOGSHP2.mol2 0 savemol2 dCOGSACP2 dCOGSACP2.mol2 0 savemol2 dCOTSHP1 dCOTSHP1.mol2 0 savemol2 dCOTSACP1 dCOTSACP1.mol2 0 savemol2 dCOTSHP2 dCOTSHP2.mol2 0 savemol2 dCOTSACP2 dCOTSACP2.mol2 0 savemol2 COASHP1 COASHP1.mol2 0 savemol2 COASACP1 COASACP1.mol2 0 savemol2 COASHP2 COASHP2.mol2 0 savemol2 COASACP2 COASACP2.mol2 0 savemol2 COCSHP1 COCSHP1.mol2 0 savemol2 COCSACP1 COCSACP1.mol2 0 savemol2 COCSHP2 COCSHP2.mol2 0 savemol2 COCSACP2 COCSACP2.mol2 0 savemol2 COGSHP1 COGSHP1.mol2 0 savemol2 COGSACP1 COGSACP1.mol2 0 savemol2 COGSHP2 COGSHP2.mol2 0 savemol2 COGSACP2 COGSACP2.mol2 0 savemol2 COUSHP1 COUSHP1.mol2 0 savemol2 COUSACP1 COUSACP1.mol2 0 savemol2 COUSHP2 COUSHP2.mol2 0 savemol2 COUSACP2 COUSACP2.mol2 0 # 4) Let's finish with cyclic-XMP X = A, C, G U and cyclic-XMP phosphorylated in position 2 CAMPP1 = seq {P1M CBO} CCMPP1 = seq {P1M CDO} CGMPP1 = seq {P1M CHO} CUMPP1 = seq {P1M CUO} CAMPP2 = seq {P2M CBO} CCMPP2 = seq {P2M CDO} CGMPP2 = seq {P2M CHO} CUMPP2 = seq {P2M CUO} set CAMPP1 name "CAMPP1" set CCMPP1 name "CCMPP1" set CGMPP1 name "CGMPP1" set CUMPP1 name "CUMPP1" set CAMPP2 name "CAMPP2" set CCMPP2 name "CCMPP2" set CGMPP2 name "CGMPP2" set CUMPP2 name "CUMPP2" saveoff CAMPP1 q4md-forcefieldtools-cofactors.off saveoff CCMPP1 q4md-forcefieldtools-cofactors.off saveoff CGMPP1 q4md-forcefieldtools-cofactors.off saveoff CUMPP1 q4md-forcefieldtools-cofactors.off saveoff CAMPP2 q4md-forcefieldtools-cofactors.off saveoff CCMPP2 q4md-forcefieldtools-cofactors.off saveoff CGMPP2 q4md-forcefieldtools-cofactors.off saveoff CUMPP2 q4md-forcefieldtools-cofactors.off # http://upjv.q4md-forcefieldtools.org/Tutorial/leap.php savemol2 CAMPP1 CAMPP1.mol2 0 savemol2 CCMPP1 CCMPP1.mol2 0 savemol2 CGMPP1 CGMPP1.mol2 0 savemol2 CUMPP1 CUMPP1.mol2 0 savemol2 CAMPP2 CAMPP2.mol2 0 savemol2 CCMPP2 CCMPP2.mol2 0 savemol2 CGMPP2 CGMPP2.mol2 0 savemol2 CUMPP2 CUMPP2.mol2 0 # http://upjv.q4md-forcefieldtools.org/Tutorial/leap-mol3.php savemol3 dAMP1 dAMP1-mol3.mol2 1 savemol3 dAMP2 dAMP2-mol3.mol2 1 savemol3 dADP1 dADP1-mol3.mol2 1 savemol3 dADP2 dADP2-mol3.mol2 1 savemol3 dATP1 dATP1-mol3.mol2 1 savemol3 dATP2 dATP2-mol3.mol2 1 savemol3 dAQP1 dAQP1-mol3.mol2 1 savemol3 dAQP2 dAQP2-mol3.mol2 1 savemol3 dCMP1 dCMP1-mol3.mol2 1 savemol3 dCMP2 dCMP2-mol3.mol2 1 savemol3 dCDP1 dCDP1-mol3.mol2 1 savemol3 dCDP2 dCDP2-mol3.mol2 1 savemol3 dCTP1 dCTP1-mol3.mol2 1 savemol3 dCTP2 dCTP2-mol3.mol2 1 savemol3 dCQP1 dCQP1-mol3.mol2 1 savemol3 dCQP2 dCQP2-mol3.mol2 1 savemol3 dGMP1 dGMP1-mol3.mol2 1 savemol3 dGMP2 dGMP2-mol3.mol2 1 savemol3 dGDP1 dGDP1-mol3.mol2 1 savemol3 dGDP2 dGDP2-mol3.mol2 1 savemol3 dGTP1 dGTP1-mol3.mol2 1 savemol3 dGTP2 dGTP2-mol3.mol2 1 savemol3 dGQP1 dGQP1-mol3.mol2 1 savemol3 dGQP2 dGQP2-mol3.mol2 1 savemol3 dTMP1 dTMP1-mol3.mol2 1 savemol3 dTMP2 dTMP2-mol3.mol2 1 savemol3 dTDP1 dTDP1-mol3.mol2 1 savemol3 dTDP2 dTDP2-mol3.mol2 1 savemol3 dTTP1 dTTP1-mol3.mol2 1 savemol3 dTTP2 dTTP2-mol3.mol2 1 savemol3 dTQP1 dTQP1-mol3.mol2 1 savemol3 dTQP2 dTQP2-mol3.mol2 1 savemol3 AMP1 AMP1-mol3.mol2 1 savemol3 AMP2 AMP2-mol3.mol2 1 savemol3 ADP1 ADP1-mol3.mol2 1 savemol3 ADP2 ADP2-mol3.mol2 1 savemol3 ATP1 ATP1-mol3.mol2 1 savemol3 ATP2 ATP2-mol3.mol2 1 savemol3 AQP1 AQP1-mol3.mol2 1 savemol3 AQP2 AQP2-mol3.mol2 1 savemol3 CMP1 CMP1-mol3.mol2 1 savemol3 CMP2 CMP2-mol3.mol2 1 savemol3 CDP1 CDP1-mol3.mol2 1 savemol3 CDP2 CDP2-mol3.mol2 1 savemol3 CTP1 CTP1-mol3.mol2 1 savemol3 CTP2 CTP2-mol3.mol2 1 savemol3 CQP1 CQP1-mol3.mol2 1 savemol3 CQP2 CQP2-mol3.mol2 1 savemol3 GMP1 GMP1-mol3.mol2 1 savemol3 GMP2 GMP2-mol3.mol2 1 savemol3 GDP1 GDP1-mol3.mol2 1 savemol3 GDP2 GDP2-mol3.mol2 1 savemol3 GTP1 GTP1-mol3.mol2 1 savemol3 GTP2 GTP2-mol3.mol2 1 savemol3 GQP1 GQP1-mol3.mol2 1 savemol3 GQP2 GQP2-mol3.mol2 1 savemol3 UMP1 UMP1-mol3.mol2 1 savemol3 UMP2 UMP2-mol3.mol2 1 savemol3 UDP1 UDP1-mol3.mol2 1 savemol3 UDP2 UDP2-mol3.mol2 1 savemol3 UTP1 UTP1-mol3.mol2 1 savemol3 UTP2 UTP2-mol3.mol2 1 savemol3 UQP1 UQP1-mol3.mol2 1 savemol3 UQP2 UQP2-mol3.mol2 1 # savemol3 AM3P1 AM3P1-mol3.mol2 1 # savemol3 AM3P2 AM3P2-mol3.mol2 1 # savemol3 AD3P1 AD3P1-mol3.mol2 1 # savemol3 AD3P2 AD3P2-mol3.mol2 1 # savemol3 AT3P1 AT3P1-mol3.mol2 1 # savemol3 AT3P2 AT3P2-mol3.mol2 1 # savemol3 AQ3P1 AQ3P1-mol3.mol2 1 # savemol3 AQ3P2 AQ3P2-mol3.mol2 1 # savemol3 EXAMPLE1 EXAMPLE1-mol3.mol2 1 # savemol3 EXAMPLE2 EXAMPLE2-mol3.mol2 1 # savemol3 EXAMPLE3 EXAMPLE3-mol3.mol2 1 savemol3 dNAD dNAD-mol3.mol2 1 savemol3 dNADH dNADH-mol3.mol2 1 savemol3 dNCD dNCD-mol3.mol2 1 savemol3 dNCDH dNCDH-mol3.mol2 1 savemol3 dNGD dNGD-mol3.mol2 1 savemol3 dNGDH dNGDH-mol3.mol2 1 savemol3 dNTD dNTD-mol3.mol2 1 savemol3 dNTDH dNTDH-mol3.mol2 1 savemol3 NAD NAD-mol3.mol2 1 savemol3 NADH NADH-mol3.mol2 1 savemol3 NCD NCD-mol3.mol2 1 savemol3 NCDH NCDH-mol3.mol2 1 savemol3 NGD NGD-mol3.mol2 1 savemol3 NGDH NGDH-mol3.mol2 1 savemol3 NUD NUD-mol3.mol2 1 savemol3 NUDH NUDH-mol3.mol2 1 savemol3 NADP1 NADP1-mol3.mol2 1 savemol3 NCDP1 NCDP1-mol3.mol2 1 savemol3 NGDP1 NGDP1-mol3.mol2 1 savemol3 NUDP1 NUDP1-mol3.mol2 1 savemol3 NADP2 NADP2-mol3.mol2 1 savemol3 NCDP2 NCDP2-mol3.mol2 1 savemol3 NGDP2 NGDP2-mol3.mol2 1 savemol3 NUDP2 NUDP2-mol3.mol2 1 savemol3 NADP1H NADP1H-mol3.mol2 1 savemol3 NCDP1H NCDP1H-mol3.mol2 1 savemol3 NGDP1H NGDP1H-mol3.mol2 1 savemol3 NUDP1H NUDP1H-mol3.mol2 1 savemol3 NADP2H NADP2H-mol3.mol2 1 savemol3 NCDP2H NCDP2H-mol3.mol2 1 savemol3 NGDP2H NGDP2H-mol3.mol2 1 savemol3 NUDP2H NUDP2H-mol3.mol2 1 savemol3 RBFLV RBFLV-mol3.mol2 1 savemol3 RBFLVH RBFLVH-mol3.mol2 1 savemol3 FMN1 FMN1-mol3.mol2 1 savemol3 FMN1H FMN1H-mol3.mol2 1 savemol3 FMN2 FMN2-mol3.mol2 1 savemol3 FMN2H FMN2H-mol3.mol2 1 savemol3 dFAD dFAD-mol3.mol2 1 savemol3 dFADH dFADH-mol3.mol2 1 savemol3 dFCD dFCD-mol3.mol2 1 savemol3 dFCDH dFCDH-mol3.mol2 1 savemol3 dFGD dFGD-mol3.mol2 1 savemol3 dFGDH dFGDH-mol3.mol2 1 savemol3 dFUD dFUD-mol3.mol2 1 savemol3 dFUDH dFUDH-mol3.mol2 1 savemol3 FAD FAD-mol3.mol2 1 savemol3 FADH FADH-mol3.mol2 1 savemol3 FCD FCD-mol3.mol2 1 savemol3 FCDH FCDH-mol3.mol2 1 savemol3 FGD FGD-mol3.mol2 1 savemol3 FGDH FGDH-mol3.mol2 1 savemol3 FUD FUD-mol3.mol2 1 savemol3 FUDH FUDH-mol3.mol2 1 savemol3 FADP1 FADP1-mol3.mol2 1 savemol3 FADHP1 FADHP1-mol3.mol2 1 savemol3 FCDP1 FCDP1-mol3.mol2 1 savemol3 FCDHP1 FCDHP1-mol3.mol2 1 savemol3 FGDP1 FGDP1-mol3.mol2 1 savemol3 FGDHP1 FGDHP1-mol3.mol2 1 savemol3 FUDP1 FUDP1-mol3.mol2 1 savemol3 FUDHP1 FUDHP1-mol3.mol2 1 savemol3 FADP2 FADP2-mol3.mol2 1 savemol3 FADHP2 FADHP2-mol3.mol2 1 savemol3 FCDP2 FCDP2-mol3.mol2 1 savemol3 FCDHP2 FCDHP2-mol3.mol2 1 savemol3 FGDP2 FGDP2-mol3.mol2 1 savemol3 FGDHP2 FGDHP2-mol3.mol2 1 savemol3 FUDP2 FUDP2-mol3.mol2 1 savemol3 FUDHP2 FUDHP2-mol3.mol2 1 savemol3 ACOA ACOA-mol3.mol2 1 savemol3 COA COA-mol3.mol2 1 savemol3 ACOAP1 ACOAP1-mol3.mol2 1 savemol3 COAP1 COAP1-mol3.mol2 1 savemol3 ACOAP2 ACOAP2-mol3.mol2 1 savemol3 COAP2 COAP2-mol3.mol2 1 savemol3 dCOASH dCOASH-mol3.mol2 1 savemol3 dCOASAC dCOASAC-mol3.mol2 1 savemol3 dCOCSH dCOCSH-mol3.mol2 1 savemol3 dCOCSAC dCOCSAC-mol3.mol2 1 savemol3 dCOGSH dCOGSH-mol3.mol2 1 savemol3 dCOGSAC dCOGSAC-mol3.mol2 1 savemol3 dCOTSH dCOTSH-mol3.mol2 1 savemol3 dCOTSAC dCOTSAC-mol3.mol2 1 savemol3 COASH COASH-mol3.mol2 1 savemol3 COASAC COASAC-mol3.mol2 1 savemol3 COCSH COCSH-mol3.mol2 1 savemol3 COCSAC COCSAC-mol3.mol2 1 savemol3 COGSH COGSH-mol3.mol2 1 savemol3 COGSAC COGSAC-mol3.mol2 1 savemol3 COUSH COUSH-mol3.mol2 1 savemol3 COUSAC COUSAC-mol3.mol2 1 savemol3 dCOASHP1 dCOASHP1-mol3.mol2 1 savemol3 dCOASACP1 dCOASACP1-mol3.mol2 1 savemol3 dCOASHP2 dCOASHP2-mol3.mol2 1 savemol3 dCOASACP2 dCOASACP2-mol3.mol2 1 savemol3 dCOCSHP1 dCOCSHP1-mol3.mol2 1 savemol3 dCOCSACP1 dCOCSACP1-mol3.mol2 1 savemol3 dCOCSHP2 dCOCSHP2-mol3.mol2 1 savemol3 dCOCSACP2 dCOCSACP2-mol3.mol2 1 savemol3 dCOGSHP1 dCOGSHP1-mol3.mol2 1 savemol3 dCOGSACP1 dCOGSACP1-mol3.mol2 1 savemol3 dCOGSHP2 dCOGSHP2-mol3.mol2 1 savemol3 dCOGSACP2 dCOGSACP2-mol3.mol2 1 savemol3 dCOTSHP1 dCOTSHP1-mol3.mol2 1 savemol3 dCOTSACP1 dCOTSACP1-mol3.mol2 1 savemol3 dCOTSHP2 dCOTSHP2-mol3.mol2 1 savemol3 dCOTSACP2 dCOTSACP2-mol3.mol2 1 savemol3 COASHP1 COASHP1-mol3.mol2 1 savemol3 COASACP1 COASACP1-mol3.mol2 1 savemol3 COASHP2 COASHP2-mol3.mol2 1 savemol3 COASACP2 COASACP2-mol3.mol2 1 savemol3 COCSHP1 COCSHP1-mol3.mol2 1 savemol3 COCSACP1 COCSACP1-mol3.mol2 1 savemol3 COCSHP2 COCSHP2-mol3.mol2 1 savemol3 COCSACP2 COCSACP2-mol3.mol2 1 savemol3 COGSHP1 COGSHP1-mol3.mol2 1 savemol3 COGSACP1 COGSACP1-mol3.mol2 1 savemol3 COGSHP2 COGSHP2-mol3.mol2 1 savemol3 COGSACP2 COGSACP2-mol3.mol2 1 savemol3 COUSHP1 COUSHP1-mol3.mol2 1 savemol3 COUSACP1 COUSACP1-mol3.mol2 1 savemol3 COUSHP2 COUSHP2-mol3.mol2 1 savemol3 COUSACP2 COUSACP2-mol3.mol2 1 savemol3 CAMPP1 CAMPP1-mol3.mol2 1 savemol3 CCMPP1 CCMPP1-mol3.mol2 1 savemol3 CGMPP1 CGMPP1-mol3.mol2 1 savemol3 CUMPP1 CUMPP1-mol3.mol2 1 savemol3 CAMPP2 CAMPP2-mol3.mol2 1 savemol3 CCMPP2 CCMPP2-mol3.mol2 1 savemol3 CGMPP2 CGMPP2-mol3.mol2 1 savemol3 CUMPP2 CUMPP2-mol3.mol2 1 ########## Activate the 196 lines below: perl -p -i.old -e 's/\#\#\#\#\#\# //g' script1.ff ###### saveamberparm dAMP1 dAMP1.top dAMP1.crd ###### saveamberparm dAMP2 dAMP2.top dAMP2.crd ###### saveamberparm dADP1 dADP1.top dADP1.crd ###### saveamberparm dADP2 dADP2.top dADP2.crd ###### saveamberparm dATP1 dATP1.top dATP1.crd ###### saveamberparm dATP2 dATP2.top dATP2.crd ###### saveamberparm dAQP1 dAQP1.top dAQP1.crd ###### saveamberparm dAQP2 dAQP2.top dAQP2.crd ###### saveamberparm dCMP1 dCMP1.top dCMP1.crd ###### saveamberparm dCMP2 dCMP2.top dCMP2.crd ###### saveamberparm dCDP1 dCDP1.top dCDP1.crd ###### saveamberparm dCDP2 dCDP2.top dCDP2.crd ###### saveamberparm dCTP1 dCTP1.top dCTP1.crd ###### saveamberparm dCTP2 dCTP2.top dCTP2.crd ###### saveamberparm dCQP1 dCQP1.top dCQP1.crd ###### saveamberparm dCQP2 dCQP2.top dCQP2.crd ###### saveamberparm dGMP1 dGMP1.top dGMP1.crd ###### saveamberparm dGMP2 dGMP2.top dGMP2.crd ###### saveamberparm dGDP1 dGDP1.top dGDP1.crd ###### saveamberparm dGDP2 dGDP2.top dGDP2.crd ###### saveamberparm dGTP1 dGTP1.top dGTP1.crd ###### saveamberparm dGTP2 dGTP2.top dGTP2.crd ###### saveamberparm dGQP1 dGQP1.top dGQP1.crd ###### saveamberparm dGQP2 dGQP2.top dGQP2.crd ###### saveamberparm dTMP1 dTMP1.top dTMP1.crd ###### saveamberparm dTMP2 dTMP2.top dTMP2.crd ###### saveamberparm dTDP1 dTDP1.top dTDP1.crd ###### saveamberparm dTDP2 dTDP2.top dTDP2.crd ###### saveamberparm dTTP1 dTTP1.top dTTP1.crd ###### saveamberparm dTTP2 dTTP2.top dTTP2.crd ###### saveamberparm dTQP1 dTQP1.top dTQP1.crd ###### saveamberparm dTQP2 dTQP2.top dTQP2.crd ###### saveamberparm AMP1 AMP1.top AMP1.crd ###### saveamberparm AMP2 AMP2.top AMP2.crd ###### saveamberparm ADP1 ADP1.top ADP1.crd ###### saveamberparm ADP2 ADP2.top ADP2.crd ###### saveamberparm ATP1 ATP1.top ATP1.crd ###### saveamberparm ATP2 ATP2.top ATP2.crd ###### saveamberparm AQP1 AQP1.top AQP1.crd ###### saveamberparm AQP2 AQP2.top AQP2.crd ###### saveamberparm CMP1 CMP1.top CMP1.crd ###### saveamberparm CMP2 CMP2.top CMP2.crd ###### saveamberparm CDP1 CDP1.top CDP1.crd ###### saveamberparm CDP2 CDP2.top CDP2.crd ###### saveamberparm CTP1 CTP1.top CTP1.crd ###### saveamberparm CTP2 CTP2.top CTP2.crd ###### saveamberparm CQP1 CQP1.top CQP1.crd ###### saveamberparm CQP2 CQP2.top CQP2.crd ###### saveamberparm GMP1 GMP1.top GMP1.crd ###### saveamberparm GMP2 GMP2.top GMP2.crd ###### saveamberparm GDP1 GDP1.top GDP1.crd ###### saveamberparm GDP2 GDP2.top GDP2.crd ###### saveamberparm GTP1 GTP1.top GTP1.crd ###### saveamberparm GTP2 GTP2.top GTP2.crd ###### saveamberparm GQP1 GQP1.top GQP1.crd ###### saveamberparm GQP2 GQP2.top GQP2.crd ###### saveamberparm UMP1 UMP1.top UMP1.crd ###### saveamberparm UMP2 UMP2.top UMP2.crd ###### saveamberparm UDP1 UDP1.top UDP1.crd ###### saveamberparm UDP2 UDP2.top UDP2.crd ###### saveamberparm UTP1 UTP1.top UTP1.crd ###### saveamberparm UTP2 UTP2.top UTP2.crd ###### saveamberparm UQP1 UQP1.top UQP1.crd ###### saveamberparm UQP2 UQP2.top UQP2.crd ###### # saveamberparm AM3P1 AM3P1.top AM3P1.crd ###### # saveamberparm AM3P2 AM3P2.top AM3P2.crd ###### # saveamberparm AD3P1 AD3P1.top AD3P1.crd ###### # saveamberparm AD3P2 AD3P2.top AD3P2.crd ###### # saveamberparm AT3P1 AT3P1.top AT3P1.crd ###### # saveamberparm AT3P2 AT3P2.top AT3P2.crd ###### # saveamberparm AQ3P1 AQ3P1.top AQ3P1.crd ###### # saveamberparm AQ3P2 AQ3P2.top AQ3P2.crd ###### # saveamberparm EXAMPLE1 EXAMPLE1.top EXAMPLE1.crd ###### # saveamberparm EXAMPLE2 EXAMPLE2.top EXAMPLE2.crd ###### # saveamberparm EXAMPLE3 EXAMPLE3.top EXAMPLE3.crd ###### saveamberparm dNAD dNAD.top dNAD.crd ###### saveamberparm dNADH dNADH.top dNADH.crd ###### saveamberparm dNCD dNCD.top dNCD.crd ###### saveamberparm dNCDH dNCDH.top dNCDH.crd ###### saveamberparm dNGD dNGD.top dNGD.crd ###### saveamberparm dNGDH dNGDH.top dNGDH.crd ###### saveamberparm dNTD dNTD.top dNTD.crd ###### saveamberparm dNTDH dNTDH.top dNTDH.crd ###### saveamberparm NAD NAD.top NAD.crd ###### saveamberparm NADH NADH.top NADH.crd ###### saveamberparm NCD NCD.top NCD.crd ###### saveamberparm NCDH NCDH.top NCDH.crd ###### saveamberparm NGD NGD.top NGD.crd ###### saveamberparm NGDH NGDH.top NGDH.crd ###### saveamberparm NUD NUD.top NUD.crd ###### saveamberparm NUDH NUDH.top NUDH.crd ###### saveamberparm NADP1 NADP1.top NADP1.crd ###### saveamberparm NCDP1 NCDP1.top NCDP1.crd ###### saveamberparm NGDP1 NGDP1.top NGDP1.crd ###### saveamberparm NUDP1 NUDP1.top NUDP1.crd ###### saveamberparm NADP2 NADP2.top NADP2.crd ###### saveamberparm NCDP2 NCDP2.top NCDP2.crd ###### saveamberparm NGDP2 NGDP2.top NGDP2.crd ###### saveamberparm NUDP2 NUDP2.top NUDP2.crd ###### saveamberparm NADP1H NADP1H.top NADP1H.crd ###### saveamberparm NCDP1H NCDP1H.top NCDP1H.crd ###### saveamberparm NGDP1H NGDP1H.top NGDP1H.crd ###### saveamberparm NUDP1H NUDP1H.top NUDP1H.crd ###### saveamberparm NADP2H NADP2H.top NADP2H.crd ###### saveamberparm NCDP2H NCDP2H.top NCDP2H.crd ###### saveamberparm NGDP2H NGDP2H.top NGDP2H.crd ###### saveamberparm NUDP2H NUDP2H.top NUDP2H.crd ###### saveamberparm RBFLV RBFLV.top RBFLV.crd ###### saveamberparm RBFLVH RBFLVH.top RBFLVH.crd ###### saveamberparm FMN1 FMN1.top FMN1.crd ###### saveamberparm FMN1H FMN1H.top FMN1H.crd ###### saveamberparm FMN2 FMN2.top FMN2.crd ###### saveamberparm FMN2H FMN2H.top FMN2H.crd ###### saveamberparm dFAD dFAD.top dFAD.crd ###### saveamberparm dFADH dFADH.top dFADH.crd ###### saveamberparm dFCD dFCD.top dFCD.crd ###### saveamberparm dFCDH dFCDH.top dFCDH.crd ###### saveamberparm dFGD dFGD.top dFGD.crd ###### saveamberparm dFGDH dFGDH.top dFGDH.crd ###### saveamberparm dFUD dFUD.top dFUD.crd ###### saveamberparm dFUDH dFUDH.top dFUDH.crd ###### saveamberparm FAD FAD.top FAD.crd ###### saveamberparm FADH FADH.top FADH.crd ###### saveamberparm FCD FCD.top FCD.crd ###### saveamberparm FCDH FCDH.top FCDH.crd ###### saveamberparm FGD FGD.top FGD.crd ###### saveamberparm FGDH FGDH.top FGDH.crd ###### saveamberparm FUD FUD.top FUD.crd ###### saveamberparm FUDH FUDH.top FUDH.crd ###### saveamberparm FADP1 FADP1.top FADP1.crd ###### saveamberparm FADHP1 FADHP1.top FADHP1.crd ###### saveamberparm FCDP1 FCDP1.top FCDP1.crd ###### saveamberparm FCDHP1 FCDHP1.top FCDHP1.crd ###### saveamberparm FGDP1 FGDP1.top FGDP1.crd ###### saveamberparm FGDHP1 FGDHP1.top FGDHP1.crd ###### saveamberparm FUDP1 FUDP1.top FUDP1.crd ###### saveamberparm FUDHP1 FUDHP1.top FUDHP1.crd ###### saveamberparm FADP2 FADP2.top FADP2.crd ###### saveamberparm FADHP2 FADHP2.top FADHP2.crd ###### saveamberparm FCDP2 FCDP2.top FCDP2.crd ###### saveamberparm FCDHP2 FCDHP2.top FCDHP2.crd ###### saveamberparm FGDP2 FGDP2.top FGDP2.crd ###### saveamberparm FGDHP2 FGDHP2.top FGDHP2.crd ###### saveamberparm FUDP2 FUDP2.top FUDP2.crd ###### saveamberparm FUDHP2 FUDHP2.top FUDHP2.crd ###### saveamberparm ACOA ACOA.top ACOA.crd ###### saveamberparm COA COA.top COA.crd ###### saveamberparm ACOAP1 ACOAP1.top ACOAP1.crd ###### saveamberparm COAP1 COAP1.top COAP1.crd ###### saveamberparm ACOAP2 ACOAP2.top ACOAP2.crd ###### saveamberparm COAP2 COAP2.top COAP2.crd ###### saveamberparm dCOASH dCOASH.top dCOASH.crd ###### saveamberparm dCOASAC dCOASAC.top dCOASAC.crd ###### saveamberparm dCOCSH dCOCSH.top dCOCSH.crd ###### saveamberparm dCOCSAC dCOCSAC.top dCOCSAC.crd ###### saveamberparm dCOGSH dCOGSH.top dCOGSH.crd ###### saveamberparm dCOGSAC dCOGSAC.top dCOGSAC.crd ###### saveamberparm dCOTSH dCOTSH.top dCOTSH.crd ###### saveamberparm dCOTSAC dCOTSAC.top dCOTSAC.crd ###### saveamberparm COASH COASH.top COASH.crd ###### saveamberparm COASAC COASAC.top COASAC.crd ###### saveamberparm COCSH COCSH.top COCSH.crd ###### saveamberparm COCSAC COCSAC.top COCSAC.crd ###### saveamberparm COGSH COGSH.top COGSH.crd ###### saveamberparm COGSAC COGSAC.top COGSAC.crd ###### saveamberparm COUSH COUSH.top COUSH.crd ###### saveamberparm COUSAC COUSAC.top COUSAC.crd ###### saveamberparm dCOASHP1 dCOASHP1.top dCOASHP1.crd ###### saveamberparm dCOASACP1 dCOASACP1.top dCOASACP1.crd ###### saveamberparm dCOASHP2 dCOASHP2.top dCOASHP2.crd ###### saveamberparm dCOASACP2 dCOASACP2.top dCOASACP2.crd ###### saveamberparm dCOCSHP1 dCOCSHP1.top dCOCSHP1.crd ###### saveamberparm dCOCSACP1 dCOCSACP1.top dCOCSACP1.crd ###### saveamberparm dCOCSHP2 dCOCSHP2.top dCOCSHP2.crd ###### saveamberparm dCOCSACP2 dCOCSACP2.top dCOCSACP2.crd ###### saveamberparm dCOGSHP1 dCOGSHP1.top dCOGSHP1.crd ###### saveamberparm dCOGSACP1 dCOGSACP1.top dCOGSACP1.crd ###### saveamberparm dCOGSHP2 dCOGSHP2.top dCOGSHP2.crd ###### saveamberparm dCOGSACP2 dCOGSACP2.top dCOGSACP2.crd ###### saveamberparm dCOTSHP1 dCOTSHP1.top dCOTSHP1.crd ###### saveamberparm dCOTSACP1 dCOTSACP1.top dCOTSACP1.crd ###### saveamberparm dCOTSHP2 dCOTSHP2.top dCOTSHP2.crd ###### saveamberparm dCOTSACP2 dCOTSACP2.top dCOTSACP2.crd ###### saveamberparm COASHP1 COASHP1.top COASHP1.crd ###### saveamberparm COASACP1 COASACP1.top COASACP1.crd ###### saveamberparm COASHP2 COASHP2.top COASHP2.crd ###### saveamberparm COASACP2 COASACP2.top COASACP2.crd ###### saveamberparm COCSHP1 COCSHP1.top COCSHP1.crd ###### saveamberparm COCSACP1 COCSACP1.top COCSACP1.crd ###### saveamberparm COCSHP2 COCSHP2.top COCSHP2.crd ###### saveamberparm COCSACP2 COCSACP2.top COCSACP2.crd ###### saveamberparm COGSHP1 COGSHP1.top COGSHP1.crd ###### saveamberparm COGSACP1 COGSACP1.top COGSACP1.crd ###### saveamberparm COGSHP2 COGSHP2.top COGSHP2.crd ###### saveamberparm COGSACP2 COGSACP2.top COGSACP2.crd ###### saveamberparm COUSHP1 COUSHP1.top COUSHP1.crd ###### saveamberparm COUSACP1 COUSACP1.top COUSACP1.crd ###### saveamberparm COUSHP2 COUSHP2.top COUSHP2.crd ###### saveamberparm COUSACP2 COUSACP2.top COUSACP2.crd ###### saveamberparm CAMPP1 CAMPP1.top CAMPP1.crd ###### saveamberparm CCMPP1 CCMPP1.top CCMPP1.crd ###### saveamberparm CGMPP1 CGMPP1.top CGMPP1.crd ###### saveamberparm CUMPP1 CUMPP1.top CUMPP1.crd ###### saveamberparm CAMPP2 CAMPP2.top CAMPP2.crd ###### saveamberparm CCMPP2 CCMPP2.top CCMPP2.crd ###### saveamberparm CGMPP2 CGMPP2.top CGMPP2.crd ###### saveamberparm CUMPP2 CUMPP2.top CUMPP2.crd quit