R.E.DD.B.: code W-74

Upload 12-01-2006 14:00 (Day-Month-Year, Paris time)
Update 28-09-2011 16:00 (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

Glycosylamine

Nucleobase

Ribose

RNA

Ribonucleic acid

Abstract

RESP atomic charges for the four nucleosides of RNA, i. e. 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.) based on the Connolly surface algorithm and the HF/6-31G* theory level. Charges suitable for MD simulations using the Cornell et al. AMBER force field (and/or its adaptations). Charges derived using 1 mol. conformation and 6 mol. orientations (Rigid-Body Reorientation Algorithm). Charge values to be compared with those reported in the projects W-75, W-76, W-77 and W-78 and compatible with the project W-69 (DNA nucleosides).

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 WHOLE MOLECULE

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	Adenosine
2	Cytidine
3	Guanosine
4	Uridine

Number of molecule(s) used in the charge derivation procedure 4

File(s) provided to the PDB format

No	Molecule name	Conformation No	Reorientation procedure	Mol. orientation No
1	Adenosine	1	Rigid Body Reorient Algo	6
2	Cytidine	1	Rigid Body Reorient Algo	6
3	Guanosine	1	Rigid Body Reorient Algo	6
4	Uridine	1	Rigid Body Reorient Algo	6

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...

Download the whole project...