R.E.DD.B.: code F-50

Upload 13-01-2006 10:26 (Day-Month-Year, Paris time)

Information about the Author (who submitted the project in R.E.DD.B.)

Firstname Francois-Yves

Lastname Dupradeau

Institute Faculte de Pharmacie, UPJV

City Amiens

Country FRANCE

General information about the Project

Molecule keywords

Nucleobase

Deoxyribose

Phosphate

Nucleotide

DNA

Abstract

RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G* theory level for the 16 components of a force field topology database useful for modeling regular DNA. 52 structures, i. e. Dimethylphosphate (conformation gauche, gauche; 4 mol. orientations) and the 4 DNA nucleosides [Deoxyadenosine, Deoxycytidine, Deoxyguanosine and Deoxythymidine (conformations C2'endo and C3'endo; 6 mol. orientations for each conformation) are used in the charge derivation. Procedure automatically carried out using the R.E.D.-III program (mol. orientation controlled using the rigid-body re-orientation algorithm implemented in R.E.D.). Charges are similar that those calculated in the Cornell et al. AMBER force field (and/or its adaptations, see Cieplak et al. J. Comput. Chem. 1995, 16, 1357-1377) althought these new values present the advantage to be highly reproducible. Charge values to be compared with those reported in the projects F-45, F-46, F-47, F-48 and F49 and compatible with the project F-56 (RNA force field topology database). The difference between the projects F-50 and F-45 is that the phosphate group is located at the position O3' and O5', respectively.
Authors of the project
F.-Y. Dupradeau, A. Pigache, T. Zaffran, R. Lelong, N. Grivel & P. Cieplak

Is the project published NOT YET

"Whole molecule" or "Molecule fragment" type projectMOLECULE FRAGMENT

Interface R.E.D. used ? YES

Charge derivation procedure

Number of Tripos mol2 file(s) provided by the author(s) 16

Contain charge values & information about molecular topology

No	Name	Download	Wikipedia	3D visualization
1	Fragment DA3
2	Fragment DA5
3	Fragment DA
4	Fragment DAN
5	Fragment DC3
6	Fragment DC5
7	Fragment DC
8	Fragment DCN
9	Fragment DG3
10	Fragment DG5
11	Fragment DG
12	Fragment DGN
13	Fragment DT3
14	Fragment DT5
15	Fragment DT
16	Fragment DTN

Number of molecule(s) used in the charge derivation procedure 5

File(s) provided to the PDB format

No	Molecule name	Conformation No	Reorientation procedure	Mol. orientation No
1	Dimethylphosphate	1	Rigid Body Reorient Algo	4
2	Deoxyadenosine	2	Rigid Body Reorient Algo	6
3	Deoxycytidine	2	Rigid Body Reorient Algo	6
4	Deoxyguanosine	2	Rigid Body Reorient Algo	6
5	Deoxythymidine	2	Rigid Body Reorient Algo	6

Information regarding Quantum Calculations

Geometry optimization

Program 1 GAUSSIAN 1998

Theory level 1 HF

More information 1 Opt=VTight

Basis set 1 6-31G*

Molecular electrostatic potential computation

Program 2 GAUSSIAN 1998

Theory level 2 HF

More information 2 IOp(6/33=2) NoSymm

Basis set 2 6-31G*

Algorithm CONNOLY SURFACE

Information about the charge fit

Program RESP

Number of stage(s) 2

input of stage 1

input of stage 2

Files the author of the project wishes to provide...

A script to convert Tripos mol2 file(s) into LEaP OFF library(ies) (for AMBER)...

A script to convert Tripos mol2 file(s) into RTF or PSF library(ies) (for CHARMM)...

A file to provide new force field parameters compatible with the Tripos mol2 file(s)...

A file (choice made by the author) to provide more information about the project...

Download the whole project...