R.E.DD.B.: code F-57

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 Display 1	3D Display 2
1	Fragment ABA3
2	Fragment ABA5
3	Fragment ABA
4	Fragment ABAN

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
2	(2R,3S)-3-Hydroxy-2-hydroxymethyl-tetrahydrofurane	1	QM Reorient Algo GAUSSIAN	1

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...

Download the whole project...