logFile leap-mol2tooff.log source leaprc.glycam04 addAtomTypes { { "CC" "C" "sp2" } { "CD" "C" "sp2" } { "CG" "C" "sp3" } { "HO" "H" "sp3" } { "H1" "H" "sp3" } { "H2" "H" "sp3" } { "HC" "H" "sp3" } { "H4" "H" "sp3" } { "OH" "O" "sp3" } { "OS" "O" "sp3" } { "NA" "N" "sp2" } { "NC" "N" "sp2" } { "ND" "N" "sp2" } } loadoff solvents.lib # To be loaded after the 'addAtomTypes' command ! FRCMOD = loadamberparams frcmod.fyd alias e edit alias q quit alias c charge alias mg measuregeom alias i impose alias seq sequence verbosity 2 # File name modification # R.E.DD.B. file name => R.E.D. IV beta file name # tripos1.mol2 => Mol_m1-o1-FG.mol2 # tripos2.mol2 => Mol_m2-o1-FG.mol2 # tripos3.mol2 => Mol_m3-o1-FG-C6.mol2 # tripos4.mol2 => Mol_m3-o1-FG-C.mol2 # tripos5.mol2 => Mol_m3-o1-FG-T6.mol2 # tripos6.mol2 => Mol_m3-o1-FG-T.mol2 # tripos7.mol2 => Mol_m4-o1-FG-C6.mol2 # tripos8.mol2 => Mol_m4-o1-FG-C.mol2 # tripos9.mol2 => Mol_m4-o1-FG-T6.mol2 # tripos10.mol2 => Mol_m4-o1-FG-T.mol2 # tripos11.mol2 => Mol_m5-o1-FG-C6.mol2 # tripos12.mol2 => Mol_m5-o1-FG-C.mol2 # tripos13.mol2 => Mol_m5-o1-FG-T6.mol2 # tripos14.mol2 => Mol_m5-o1-FG-T.mol2 # UNIT 1 AMN = loadmol2 Mol_m1-o1-FG.mol2 # 1st conformation loaded # AMN = loadmol2 Mol_m1-o2-FG.mol2 # 2nd conformation not loaded set AMN name "AMN" # set AMN head AMN.1.O6' set AMN tail AMN.1.O1' set AMN.1 connect0 AMN.1.O6' set AMN.1 connect1 AMN.1.O1' set AMN.1 restype saccharide set AMN.1 name "AMN" # set FF atom types set AMN.1.C1' type CG set AMN.1.H1' type H2 set AMN.1.O1' type OS set AMN.1.C2' type CG set AMN.1.H2' type H1 set AMN.1.O2' type OH set AMN.1.HO2' type HO set AMN.1.C3' type CG set AMN.1.H3' type H1 set AMN.1.O3' type OH set AMN.1.HO3' type HO set AMN.1.C4' type CG set AMN.1.H4' type H1 set AMN.1.O4' type OH set AMN.1.HO4' type HO set AMN.1.C5' type CG set AMN.1.H5' type H1 set AMN.1.O5' type OS set AMN.1.C6' type CG set AMN.1.H61' type H1 set AMN.1.H62' type H1 set AMN.1.O6' type OH set AMN.1.HO6' type HO saveoff AMN AMN.off # UNIT 2 LNK = loadmol2 Mol_m2-o1-FG.mol2 # 1st conformation loaded # LNK = loadmol2 Mol_m2-o2-FG.mol2 # 2nd conformation not loaded set LNK name "LNK" set LNK head LNK.1.C1 set LNK tail LNK.1.N6 set LNK.1 connect0 LNK.1.C1 set LNK.1 connect1 LNK.1.N6 set LNK.1 restype undefined set LNK.1 name "LNK" # set FF atom types set LNK.1.C1 type CG set LNK.1.H11 type H1 set LNK.1.H12 type H1 set LNK.1.C2 type CG set LNK.1.H21 type HC set LNK.1.H22 type HC set LNK.1.C3 type CC set LNK.1.N4 type NC set LNK.1.N5 type ND set LNK.1.N6 type NA set LNK.1.C7 type CD set LNK.1.H7 type H4 saveoff LNK LNK.off # UNIT 3a AMC = loadmol2 Mol_m3-o1-FG-C.mol2 # 1st conformation loaded # AMC = loadmol2 Mol_m3-o2-FG-C.mol2 # 2nd conformation not loaded set AMC name "AMC" set AMC head AMC.1.C4' set AMC tail AMC.1.O1' set AMC.1 connect0 AMC.1.C4' set AMC.1 connect1 AMC.1.O1' set AMC.1 restype saccharide set AMC.1 name "AMC" # set FF atom types set AMC.1.C1' type CG set AMC.1.H1' type H2 set AMC.1.O1' type OS set AMC.1.C2' type CG set AMC.1.H2' type H1 set AMC.1.O2' type OH set AMC.1.HO2' type HO set AMC.1.C3' type CG set AMC.1.H3' type H1 set AMC.1.O3' type OH set AMC.1.HO3' type HO set AMC.1.C4' type CG set AMC.1.H4' type H1 set AMC.1.C5' type CG set AMC.1.H5' type H1 set AMC.1.O5' type OS set AMC.1.C6' type CG set AMC.1.H61' type H1 set AMC.1.H62' type H1 saveoff AMC AMC.off # UNIT 3b AMT = loadmol2 Mol_m3-o1-FG-T.mol2 # 1st conformation loaded # AMT = loadmol2 Mol_m3-o2-FG-T.mol2 # 2nd conformation not loaded set AMT name "AMT" # set AMT head AMT.1.C4' set AMT tail AMT.1.O1' set AMT.1 connect0 AMT.1.C4' set AMT.1 connect1 AMT.1.O1' set AMT.1 restype saccharide set AMT.1 name "AMT" # set FF atom types set AMT.1.C1' type CG set AMT.1.H1' type H2 set AMT.1.O1' type OS set AMT.1.C2' type CG set AMT.1.H2' type H1 set AMT.1.O2' type OH set AMT.1.HO2' type HO set AMT.1.C3' type CG set AMT.1.H3' type H1 set AMT.1.O3' type OH set AMT.1.HO3' type HO set AMT.1.C4' type CG set AMT.1.H4' type H1 set AMT.1.O4' type OH set AMT.1.HO4' type HO set AMT.1.C5' type CG set AMT.1.H5' type H1 set AMT.1.O5' type OS set AMT.1.C6' type CG set AMT.1.H61' type H1 set AMT.1.H62' type H1 saveoff AMT AMT.off # UNIT 4a AGC = loadmol2 Mol_m4-o1-FG-C.mol2 # 1st conformation loaded # AGC = loadmol2 Mol_m4-o2-FG-C.mol2 # 2nd conformation not loaded set AGC name "AGC" set AGC head AGC.1.C4' set AGC tail AGC.1.C1' set AGC.1 connect0 AGC.1.C4' set AGC.1 connect1 AGC.1.C1' set AGC.1 restype saccharide set AGC.1 name "AGC" # set FF atom types set AGC.1.C1' type CG set AGC.1.H1' type H2 set AGC.1.C2' type CG set AGC.1.H2' type H1 set AGC.1.O2' type OH set AGC.1.HO2' type HO set AGC.1.C3' type CG set AGC.1.H3' type H1 set AGC.1.O3' type OH set AGC.1.HO3' type HO set AGC.1.C4' type CG set AGC.1.H4' type H1 set AGC.1.C5' type CG set AGC.1.H5' type H1 set AGC.1.O5' type OS set AGC.1.C6' type CG set AGC.1.H61' type H1 set AGC.1.H62' type H1 saveoff AGC AGC.off # UNIT 4b AGT = loadmol2 Mol_m4-o1-FG-T.mol2 # 1st conformation loaded # AGT = loadmol2 Mol_m4-o2-FG-T.mol2 # 2nd conformation not loaded set AGT name "AGT" set AGT head AGT.1.C4' # set AGT tail AGT.1.C1' set AGT.1 connect0 AGT.1.C4' set AGT.1 connect1 AGT.1.C1' set AGT.1 restype saccharide set AGT.1 name "AGT" # set FF atom types set AGT.1.C1' type CG set AGT.1.H1' type H2 set AGT.1.O1' type OH set AGT.1.HO1' type HO set AGT.1.C2' type CG set AGT.1.H2' type H1 set AGT.1.O2' type OH set AGT.1.HO2' type HO set AGT.1.C3' type CG set AGT.1.H3' type H1 set AGT.1.O3' type OH set AGT.1.HO3' type HO set AGT.1.C4' type CG set AGT.1.H4' type H1 set AGT.1.C5' type CG set AGT.1.H5' type H1 set AGT.1.O5' type OS set AGT.1.C6' type CG set AGT.1.H61' type H1 set AGT.1.H62' type H1 saveoff AGT AGT.off # UNIT 5a BGC = loadmol2 Mol_m5-o1-FG-C.mol2 # 1st conformation loaded # BGC = loadmol2 Mol_m5-o2-FG-C.mol2 # 2nd conformation not loaded set BGC name "BGC" set BGC head BGC.1.C4' set BGC tail BGC.1.C1' set BGC.1 connect0 BGC.1.C4' set BGC.1 connect1 BGC.1.C1' set BGC.1 restype saccharide set BGC.1 name "BGC" # set FF atom types set BGC.1.C1' type CG set BGC.1.H1' type H2 set BGC.1.C2' type CG set BGC.1.H2' type H1 set BGC.1.O2' type OH set BGC.1.HO2' type HO set BGC.1.C3' type CG set BGC.1.H3' type H1 set BGC.1.O3' type OH set BGC.1.HO3' type HO set BGC.1.C4' type CG set BGC.1.H4' type H1 set BGC.1.C5' type CG set BGC.1.H5' type H1 set BGC.1.O5' type OS set BGC.1.C6' type CG set BGC.1.H61' type H1 set BGC.1.H62' type H1 saveoff BGC BGC.off # UNIT 5b BGT = loadmol2 Mol_m5-o1-FG-T.mol2 # 1st conformation loaded # BGT = loadmol2 Mol_m5-o2-FG-T.mol2 # 2nd conformation not loaded set BGT name "BGT" set BGT head BGT.1.C4' # set BGT tail BGT.1.C1' set BGT.1 connect0 BGT.1.C4' set BGT.1 connect1 BGT.1.C1' set BGT.1 restype saccharide set BGT.1 name "BGT" # set FF atom types set BGT.1.C1' type CG set BGT.1.H1' type H2 set BGT.1.O1' type OH set BGT.1.HO1' type HO set BGT.1.C2' type CG set BGT.1.H2' type H1 set BGT.1.O2' type OH set BGT.1.HO2' type HO set BGT.1.C3' type CG set BGT.1.H3' type H1 set BGT.1.O3' type OH set BGT.1.HO3' type HO set BGT.1.C4' type CG set BGT.1.H4' type H1 set BGT.1.C5' type CG set BGT.1.H5' type H1 set BGT.1.O5' type OS set BGT.1.C6' type CG set BGT.1.H61' type H1 set BGT.1.H62' type H1 saveoff BGT BGT.off ######################################### # 6 following units loaded for information but not used ######################################### # UNIT 3a-6OH AMC6 = loadmol2 Mol_m3-o1-FG-C6.mol2 # 1st conformation loaded # AMC6 = loadmol2 Mol_m3-o2-FG-C6.mol2 # 2nd conformation not loaded set AMC6 name "AMC6" set AMC6 head AMC6.1.C4' set AMC6 tail AMC6.1.O1' set AMC6.1 connect0 AMC6.1.C4' set AMC6.1 connect1 AMC6.1.O1' set AMC6.1 restype saccharide set AMC6.1 name "AMC6" # set FF atom types set AMC6.1.C1' type CG set AMC6.1.H1' type H2 set AMC6.1.O1' type OS set AMC6.1.C2' type CG set AMC6.1.H2' type H1 set AMC6.1.O2' type OH set AMC6.1.HO2' type HO set AMC6.1.C3' type CG set AMC6.1.H3' type H1 set AMC6.1.O3' type OH set AMC6.1.HO3' type HO set AMC6.1.C4' type CG set AMC6.1.H4' type H1 set AMC6.1.C5' type CG set AMC6.1.H5' type H1 set AMC6.1.O5' type OS set AMC6.1.C6' type CG set AMC6.1.H61' type H1 set AMC6.1.H62' type H1 set AMC6.1.O6' type OH set AMC6.1.HO6' type HO saveoff AMC6 AMC6.off # UNIT 3b-6OH AMT6 = loadmol2 Mol_m3-o1-FG-T6.mol2 # 1st conformation loaded # AMT6 = loadmol2 Mol_m3-o2-FG-T6.mol2 # 2nd conformation not loaded set AMT6 name "AMT6" # set AMT6 head AMT6.1.C4' set AMT6 tail AMT6.1.O1' set AMT6.1 connect0 AMT6.1.C4' set AMT6.1 connect1 AMT6.1.O1' set AMT6.1 restype saccharide set AMT6.1 name "AMT6" # set FF atom types set AMT6.1.C1' type CG set AMT6.1.H1' type H2 set AMT6.1.O1' type OS set AMT6.1.C2' type CG set AMT6.1.H2' type H1 set AMT6.1.O2' type OH set AMT6.1.HO2' type HO set AMT6.1.C3' type CG set AMT6.1.H3' type H1 set AMT6.1.O3' type OH set AMT6.1.HO3' type HO set AMT6.1.C4' type CG set AMT6.1.H4' type H1 set AMT6.1.O4' type OH set AMT6.1.HO4' type HO set AMT6.1.C5' type CG set AMT6.1.H5' type H1 set AMT6.1.O5' type OS set AMT6.1.C6' type CG set AMT6.1.H61' type H1 set AMT6.1.H62' type H1 set AMT6.1.O6' type OH set AMT6.1.HO6' type HO saveoff AMT6 AMT6.off # UNIT 4a-6OH AGC6 = loadmol2 Mol_m4-o1-FG-C6.mol2 # 1st conformation loaded # AGC6 = loadmol2 Mol_m4-o2-FG-C6.mol2 # 2nd conformation not loaded set AGC6 name "AGC6" set AGC6 head AGC6.1.C4' set AGC6 tail AGC6.1.C1' set AGC6.1 connect0 AGC6.1.C4' set AGC6.1 connect1 AGC6.1.C1' set AGC6.1 restype saccharide set AGC6.1 name "AGC6" # set FF atom types set AGC6.1.C1' type CG set AGC6.1.H1' type H2 set AGC6.1.C2' type CG set AGC6.1.H2' type H1 set AGC6.1.O2' type OH set AGC6.1.HO2' type HO set AGC6.1.C3' type CG set AGC6.1.H3' type H1 set AGC6.1.O3' type OH set AGC6.1.HO3' type HO set AGC6.1.C4' type CG set AGC6.1.H4' type H1 set AGC6.1.C5' type CG set AGC6.1.H5' type H1 set AGC6.1.O5' type OS set AGC6.1.C6' type CG set AGC6.1.H61' type H1 set AGC6.1.H62' type H1 set AGC6.1.O6' type OH set AGC6.1.HO6' type HO saveoff AGC6 AGC6.off # UNIT 4b-6OH AGT6 = loadmol2 Mol_m4-o1-FG-T6.mol2 # 1st conformation loaded # AGT6 = loadmol2 Mol_m4-o2-FG-T6.mol2 # 2nd conformation not loaded set AGT6 name "AGT6" set AGT6 head AGT6.1.C4' # set AGT6 tail AGT6.1.C1' set AGT6.1 connect0 AGT6.1.C4' set AGT6.1 connect1 AGT6.1.C1' set AGT6.1 restype saccharide set AGT6.1 name "AGT6" # set FF atom types set AGT6.1.C1' type CG set AGT6.1.H1' type H2 set AGT6.1.O1' type OH set AGT6.1.HO1' type HO set AGT6.1.C2' type CG set AGT6.1.H2' type H1 set AGT6.1.O2' type OH set AGT6.1.HO2' type HO set AGT6.1.C3' type CG set AGT6.1.H3' type H1 set AGT6.1.O3' type OH set AGT6.1.HO3' type HO set AGT6.1.C4' type CG set AGT6.1.H4' type H1 set AGT6.1.C5' type CG set AGT6.1.H5' type H1 set AGT6.1.O5' type OS set AGT6.1.C6' type CG set AGT6.1.H61' type H1 set AGT6.1.H62' type H1 set AGT6.1.O6' type OH set AGT6.1.HO6' type HO saveoff AGT6 AGT6.off # UNIT 5a-6OH BGC6 = loadmol2 Mol_m5-o1-FG-C6.mol2 # 1st conformation loaded # BGC6 = loadmol2 Mol_m5-o2-FG-C6.mol2 # 2nd conformation not loaded set BGC6 name "BGC6" set BGC6 head BGC6.1.C4' set BGC6 tail BGC6.1.C1' set BGC6.1 connect0 BGC6.1.C4' set BGC6.1 connect1 BGC6.1.C1' set BGC6.1 restype saccharide set BGC6.1 name "BGC6" # set FF atom types set BGC6.1.C1' type CG set BGC6.1.H1' type H2 set BGC6.1.C2' type CG set BGC6.1.H2' type H1 set BGC6.1.O2' type OH set BGC6.1.HO2' type HO set BGC6.1.C3' type CG set BGC6.1.H3' type H1 set BGC6.1.O3' type OH set BGC6.1.HO3' type HO set BGC6.1.C4' type CG set BGC6.1.H4' type H1 set BGC6.1.C5' type CG set BGC6.1.H5' type H1 set BGC6.1.O5' type OS set BGC6.1.C6' type CG set BGC6.1.H61' type H1 set BGC6.1.H62' type H1 set BGC6.1.O6' type OH set BGC6.1.HO6' type HO saveoff BGC6 BGC6.off # UNIT 5b-6OH BGT6 = loadmol2 Mol_m5-o1-FG-T6.mol2 # 1st conformation loaded # BGT6 = loadmol2 Mol_m5-o2-FG-T6.mol2 # 2nd conformation not loaded set BGT6 name "BGT6" set BGT6 head BGT6.1.C4' # set BGT6 tail BGT6.1.C1' set BGT6.1 connect0 BGT6.1.C4' set BGT6.1 connect1 BGT6.1.C1' set BGT6.1 restype saccharide set BGT6.1 name "BGT6" # set FF atom types set BGT6.1.C1' type CG set BGT6.1.H1' type H2 set BGT6.1.O1' type OH set BGT6.1.HO1' type HO set BGT6.1.C2' type CG set BGT6.1.H2' type H1 set BGT6.1.O2' type OH set BGT6.1.HO2' type HO set BGT6.1.C3' type CG set BGT6.1.H3' type H1 set BGT6.1.O3' type OH set BGT6.1.HO3' type HO set BGT6.1.C4' type CG set BGT6.1.H4' type H1 set BGT6.1.C5' type CG set BGT6.1.H5' type H1 set BGT6.1.O5' type OS set BGT6.1.C6' type CG set BGT6.1.H61' type H1 set BGT6.1.H62' type H1 set BGT6.1.O6' type OH set BGT6.1.HO6' type HO saveoff BGT6 BGT6.off c AMN c LNK c AMC c AMT c AGC c AGT c BGC c BGT # Not used in this script c AMC6 c AMT6 c AGC6 c AGT6 c BGC6 c BGT6 U = seq {AMN LNK} set U head U.2.N6 # Oligosaccharide 1-b A1 = seq {AMT BGT} set A1 tail A1.1.C6' A2 = seq {A1 U} set A2 tail A2.2.C6' O1 = seq {A2 U} # Oligosaccharide 2-a B1 = seq {AMT AGT} set B1 tail B1.1.C6' B2 = seq {B1 U} set B2 tail B2.2.C6' O2 = seq {B2 U} # Oligosaccharide 3-b C1 = seq {AMT AMC BGT} set C1 tail C1.1.C6' C2 = seq {C1 U} set C2 tail C2.2.C6' C3 = seq {C2 U} set C3 tail C3.3.C6' O3 = seq {C3 U} # Oligosaccharide 4-a D1 = seq {AMT AMC AGT} set D1 tail D1.1.C6' D2 = seq {D1 U} set D2 tail D2.2.C6' D3 = seq {D2 U} set D3 tail D3.3.C6' O4 = seq {D3 U} # Oligosaccharide 5-b E1 = seq {AMT BGC} set E1 tail E1.1.C6' E2 = seq {E1 U} set E2 tail E2.2.C6' E3 = seq {E2 U} set E3 tail E3.2.C1' O5 = seq {E3 U} # Oligosaccharide 7-a F1 = seq {AMT AGC} set F1 tail F1.1.C6' F2 = seq {F1 U} set F2 tail F2.2.C6' F3 = seq {F2 U} set F3 tail F3.2.C1' O7 = seq {F3 U} # Oligosaccharide 6-b G1 = seq {AMT AMC BGC} set G1 tail G1.1.C6' G2 = seq {G1 U} set G2 tail G2.2.C6' G3 = seq {G2 U} set G3 tail G3.3.C6' G4 = seq {G3 U} set G4 tail G4.3.C1' O6 = seq {G4 U} # Oligosaccharide 8-a G1 = seq {AMT AMC AGC} set G1 tail G1.1.C6' G2 = seq {G1 U} set G2 tail G2.2.C6' G3 = seq {G2 U} set G3 tail G3.3.C6' G4 = seq {G3 U} set G4 tail G4.3.C1' O8 = seq {G4 U} # Oligo-X X1 = seq {AMT AMC AMC AMC AMC AMC AMC AMC AMC AGC} set X1 tail X1.1.C6' X2 = seq {X1 U} set X2 tail X2.2.C6' X3 = seq {X2 U} set X3 tail X3.3.C6' X4 = seq {X3 U} set X4 tail X4.4.C6' X5 = seq {X4 U} set X5 tail X5.5.C6' X6 = seq {X5 U} set X6 tail X6.6.C6' X7 = seq {X6 U} set X7 tail X7.7.C6' X8 = seq {X7 U} set X8 tail X8.8.C6' X9 = seq {X8 U} set X9 tail X9.9.C6' X10 = seq {X9 U} set X10 tail X10.10.C6' X11 = seq {X10 U} set X11 tail X11.10.C1' OX = seq {X11 U} c O1 c O2 c O3 c O4 c O5 c O6 c O7 c O8 c OX savepdb O1 O1.pdb savepdb O2 O2.pdb savepdb O3 O3.pdb savepdb O4 O4.pdb savepdb O5 O5.pdb savepdb O6 O6.pdb savepdb O7 O7.pdb savepdb O8 O8.pdb savepdb OX OX.pdb solvateOct O1 TIP3PBOX 10 solvateOct O2 TIP3PBOX 10 solvateOct O3 TIP3PBOX 10 solvateOct O4 TIP3PBOX 10 solvateOct O5 TIP3PBOX 10 solvateOct O6 TIP3PBOX 10 solvateOct O7 TIP3PBOX 10 solvateOct O8 TIP3PBOX 10 solvateOct OX TIP3PBOX 10 savepdb O1 O1w.pdb savepdb O2 O2w.pdb savepdb O3 O3w.pdb savepdb O4 O4w.pdb savepdb O5 O5w.pdb savepdb O6 O6w.pdb savepdb O7 O7w.pdb savepdb O8 O8w.pdb savepdb OX OXw.pdb saveamberparm O1 O1.top O1.crd saveamberparm O2 O2.top O2.crd saveamberparm O3 O3.top O3.crd saveamberparm O4 O4.top O4.crd saveamberparm O5 O5.top O5.crd saveamberparm O6 O6.top O6.crd saveamberparm O7 O7.top O7.crd saveamberparm O8 O8.top O8.crd saveamberparm OX OX.top OX.crd # q