Summary of information
Ribonucleic acid


Upload 13-01-2006 12:25 (Day-Month-Year, Paris time)
Update 28-09-2011 16:06 (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 Ribose Phosphate Nucleotide RNA


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 RNA. 28 structures, i. e. Dimethylphosphate (conformation gauche, gauche; 4 mol. orientations) 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. Charge values to be compared with those reported in the projects F-52, F-53, F-54, F-55 and F56 and compatible with the project F-45 (DNA force field topology database). The difference between the projects F-51 and F-56 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 RA3 Wiki_Logo Jmol_Logo JSmol_Logo
2 Fragment RA5 Wiki_Logo Jmol_Logo JSmol_Logo
3 Fragment RA Wiki_Logo Jmol_Logo JSmol_Logo
4 Fragment RAN Wiki_Logo Jmol_Logo JSmol_Logo
5 Fragment RC3 Wiki_Logo Jmol_Logo JSmol_Logo
6 Fragment RC5 Wiki_Logo Jmol_Logo JSmol_Logo
7 Fragment RC Wiki_Logo Jmol_Logo JSmol_Logo
8 Fragment RCN Wiki_Logo Jmol_Logo JSmol_Logo
9 Fragment RG3 Wiki_Logo Jmol_Logo JSmol_Logo
10 Fragment RG5 Wiki_Logo Jmol_Logo JSmol_Logo
11 Fragment RG Wiki_Logo Jmol_Logo JSmol_Logo
12 Fragment RGN Wiki_Logo Jmol_Logo JSmol_Logo
13 Fragment RU3 Wiki_Logo Jmol_Logo JSmol_Logo
14 Fragment RU5 Wiki_Logo Jmol_Logo JSmol_Logo
15 Fragment RU Wiki_Logo Jmol_Logo JSmol_Logo
16 Fragment RUN 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 Adenosine 1 Rigid Body Reorient Algo 6 Wiki_Logo
3 Cytidine 1 Rigid Body Reorient Algo 6 Wiki_Logo
4 Guanosine 1 Rigid Body Reorient Algo 6 Wiki_Logo
5 Uridine 1 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...

Valid XHTML 1.0 Strict CSS Valide !

Internet page © 2006-2021. All rights reserved.
Université de Picardie Jules Verne - Sanford Burnham Prebys Medical Discovery Institute.
R.E.DD.B. projects free