Summary of information
Deoxyribonucleic acid


Upload 13-01-2006 08:57 (Day-Month-Year, Paris time)
Update 28-09-2011 16:04 (Day-Month-Year, Paris time)

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

Firstname Francois-Yves

Lastname Dupradeau

Institute UFR de pharmacie, UPJV

City Amiens

Country FRANCE

General information about the Project

Molecule keywords

Nucleobase Deoxyribose Phosphate Nucleotide DNA


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-46, F-47, F-48, F-49 and F50 and compatible with the project F-51 (RNA force field topology database). The difference between the projects F-45 and F-50 is that the phosphate group is located at the position O5' and O3', respectively.

Publication YES      

Author(s) F.-Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski and P. Cieplak

Journal Phys. Chem. Chem. Phys.

Year 2010

Volume 12

Page(s) 7821-7839

"Whole molecule" or "Molecule fragment" type project MOLECULE 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 Display 1 3D Display 2
1 Fragment DA3 Wiki_Logo Jmol_Logo JSmol_Logo
2 Fragment DA5 Wiki_Logo Jmol_Logo JSmol_Logo
3 Fragment DA Wiki_Logo Jmol_Logo JSmol_Logo
4 Fragment DAN Wiki_Logo Jmol_Logo JSmol_Logo
5 Fragment DC3 Wiki_Logo Jmol_Logo JSmol_Logo
6 Fragment DC5 Wiki_Logo Jmol_Logo JSmol_Logo
7 Fragment DC Wiki_Logo Jmol_Logo JSmol_Logo
8 Fragment DCN Wiki_Logo Jmol_Logo JSmol_Logo
9 Fragment DG3 Wiki_Logo Jmol_Logo JSmol_Logo
10 Fragment DG5 Wiki_Logo Jmol_Logo JSmol_Logo
11 Fragment DG Wiki_Logo Jmol_Logo JSmol_Logo
12 Fragment DGN Wiki_Logo Jmol_Logo JSmol_Logo
13 Fragment DT3 Wiki_Logo Jmol_Logo JSmol_Logo
14 Fragment DT5 Wiki_Logo Jmol_Logo JSmol_Logo
15 Fragment DT Wiki_Logo Jmol_Logo JSmol_Logo
16 Fragment DTN Wiki_Logo Jmol_Logo JSmol_Logo

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 Download Wikipedia
1 Dimethylphosphate 1 Rigid Body Reorient Algo 4 Wiki_Logo
2 Deoxyadenosine 2 Rigid Body Reorient Algo 6 Wiki_Logo
3 Deoxycytidine 2 Rigid Body Reorient Algo 6 Wiki_Logo
4 Deoxyguanosine 2 Rigid Body Reorient Algo 6 Wiki_Logo
5 Deoxythymidine 2 Rigid Body Reorient Algo 6 Wiki_Logo

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*


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

Download the whole project...

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