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
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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