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 |
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 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
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
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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