Summary of information
PROJECT
Nucleic acid

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Upload 08-02-2006 09:17 (Day-Month-Year, Paris time)
Update 28-09-2011 16:12 (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

Pyrimidine, purine Deoxyribose, ribose Phosphate Nucleotide DNA, RNA


Abstract

RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G* theory level for the 32 components of a force field topology database useful for modeling regular DNA and RNA. 76 structures, i. e. Dimethylphosphate (conformation gauche, gauche; 4 mol. orientations), the 4 DNA nucleosides [Deoxyadenosine, Deoxycytidine, Deoxyguanosine and Deoxythymidine (conformations C2'endo and C3'endo; 6 mol. orientations for each conformation) and the 4 RNA nucleosides [Adenosine, Cytidine, Guanosine and Uridine (conformation C3'endo, dihedral constraints were used in the geometry optimization step to avoid intra-molecular hydrogen bonds and transition state type structures: HO3'-O3'-C3'-C4' = 180 deg., HO2'-O2'-C2'-C3' = 290 deg.; 6 mol. orientations) 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. Moreover, no manual adaptation of the total charge of the terminal DNA and RNA fragments is required since the DNA and RNA nucleosides are fitted in a single R.E.D. run. Charge values to be compared with those reported in the projects F-45 and F51 (DNA and RNA force field topology database, 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) 32

Contain charge values & information about molecular topology

No Name Download Wikipedia 3D visualization
1 Fragment DA3 Link Wiki Logo Jmol Logo
2 Fragment DA5 Link Wiki Logo Jmol Logo
3 Fragment DA Link Wiki Logo Jmol Logo
4 Fragment DAN Link Wiki Logo Jmol Logo
5 Fragment DC3 Link Wiki Logo Jmol Logo
6 Fragment DC5 Link Wiki Logo Jmol Logo
7 Fragment DC Link Wiki Logo Jmol Logo
8 Fragment DCN Link Wiki Logo Jmol Logo
9 Fragment DG3 Link Wiki Logo Jmol Logo
10 Fragment DG5 Link Wiki Logo Jmol Logo
11 Fragment DG Link Wiki Logo Jmol Logo
12 Fragment DGN Link Wiki Logo Jmol Logo
13 Fragment DT3 Link Wiki Logo Jmol Logo
14 Fragment DT5 Link Wiki Logo Jmol Logo
15 Fragment DT Link Wiki Logo Jmol Logo
16 Fragment DTN Link Wiki Logo Jmol Logo
17 Fragment RA3 Link Wiki Logo Jmol Logo
18 Fragment RA5 Link Wiki Logo Jmol Logo
19 Fragment RA Link Wiki Logo Jmol Logo
20 Fragment RAN Link Wiki Logo Jmol Logo
21 Fragment RC3 Link Wiki Logo Jmol Logo
22 Fragment RC5 Link Wiki Logo Jmol Logo
23 Fragment RC Link Wiki Logo Jmol Logo
24 Fragment RCN Link Wiki Logo Jmol Logo
25 Fragment RG3 Link Wiki Logo Jmol Logo
26 Fragment RG5 Link Wiki Logo Jmol Logo
27 Fragment RG Link Wiki Logo Jmol Logo
28 Fragment RGN Link Wiki Logo Jmol Logo
29 Fragment RU3 Link Wiki Logo Jmol Logo
30 Fragment RU5 Link Wiki Logo Jmol Logo
31 Fragment RU Link Wiki Logo Jmol Logo
32 Fragment RUN Link Wiki Logo Jmol Logo


Number of molecule(s) used in the charge derivation procedure 9

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 Link Wiki Logo
2 Deoxyadenosine 2 Rigid Body Reorient Algo 6 Link Wiki Logo
3 Deoxycytidine 2 Rigid Body Reorient Algo 6 Link Wiki Logo
4 Deoxyguanosine 2 Rigid Body Reorient Algo 6 Link Wiki Logo
5 Deoxythymidine 2 Rigid Body Reorient Algo 6 Link Wiki Logo
6 Adenosine 1 Rigid Body Reorient Algo 6 Link Wiki Logo
7 Cytidine 1 Rigid Body Reorient Algo 6 Link Wiki Logo
8 Guanosine 1 Rigid Body Reorient Algo 6 Link Wiki Logo
9 Uridine 1 Rigid Body Reorient Algo 6 Link 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*

Algorithm CONNOLLY SURFACE


Information about the charge fit

Program RESP

Number of stage(s) 2

input of stage 1 Link

input of stage 2 Link



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

A script to convert Tripos mol2 file(s) into LEaP OFF library(ies) (for AMBER)...Link
A script to convert Tripos mol2 file(s) into RTF or PSF library(ies) (for CHARMM)...Link
A file to provide new force field parameters compatible with the Tripos mol2 file(s)...Link
A file (choice made by the author) to provide more information about the project...Link
A file (choice made by the author) to provide more information about the project...Link

Download the whole project... Link



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