Upload 14-01-2006 08:44 (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
Model base pair |
DNA abasic site |
Ether |
Phosphate |
Unusual nucleotide |
Abstract
RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G* theory level for 4 fragments of a DNA abasic site. 2 structures, i. e. Dimethylphosphate (conformation gauche, gauche; single mol. orientation) and (2R,3S)-3-Hydroxy-2-hydroxymethyl-tetrahydrofurane (conformation C2'endo; single mol. orientation) are used in the charge derivation. Procedure automatically carried out using the R.E.D.-III program (mol. orientation generated by the QM program is conserved for each structure). Charge values suitable for MD simulations using the Cornell et al. AMBER force field (and/or its different adaptations). Charges to be used together with the project F-58 or F-59 (see the corresponding publication).
Publication YES 
Author(s) F.-Y. Dupradeau, D. A. Case, C. Yu, R. Jimenez and F. E. Romesberg
Journal J. Am. Chem. Soc.
Year 2005
Volume 127
Page(s) 15612-15617
"Whole molecule" or "Molecule fragment" type projectMOLECULE FRAGMENT
Interface R.E.D. used ? YES
Charge derivation procedure
Number of Tripos mol2 file(s) provided by the author(s) 4
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=Tight
Basis set 1 6-31G*
Molecular electrostatic potential computation
Program 2 GAUSSIAN 1998
Theory level 2 HF
More information 2 IOp(6/33=2)
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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