Summary of information
PROJECT
(2R,3S)-3-Hydroxy-2-hydroxymethyl-tetrahydrofurane nucleotide fragment

Wiki Logo

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

No Name Download Wikipedia 3D visualization
1 Fragment ABA3 Link Wiki Logo Jmol Logo
2 Fragment ABA5 Link Wiki Logo Jmol Logo
3 Fragment ABA Link Wiki Logo Jmol Logo
4 Fragment ABAN Link Wiki Logo Jmol Logo


Number of molecule(s) used in the charge derivation procedure 2

File(s) provided to the PDB format

No Molecule name Conformation No Reorientation procedure Mol. orientation No Download Wikipedia
1 Dimethylphosphate 1 QM Reorient Algo GAUSSIAN 1 Link Wiki Logo
2 (2R,3S)-3-Hydroxy-2-hydroxymethyl-tetrahydrofurane 1 QM Reorient Algo GAUSSIAN 1 Link Wiki Logo



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 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



Valid XHTML 1.0 Strict CSS Valide !

Internet page © 2006-2016. All rights reserved.
Université de Picardie Jules Verne - Sanford Burnham Prebys Medical Discovery Institute.
R.E.DD.B. projects free.