R.E.DD.B.: code W-46

Upload 23-11-2005 14:25 (Day-Month-Year, Paris time)
Update 22-11-2006 13:02 (Day-Month-Year, Paris time)

Information about the Author (who submitted the project in R.E.DD.B.)

Firstname Francois-Yves

Lastname Dupradeau

Institute Faculte de Pharmacie, UPJV

City Amiens

Country FRANCE

General information about the Project

Molecule keywords

Organic molecule

Alcohol, Ketone

Sulfoxide, Nitrile

Aromatic, Halogen

Carboxylic acid

Abstract

RESP atomic charges for 10 solvent molecules (Dimethylsulfoxide, Ethanol, Trifluoroethanol, Methanol, Acetone, Acetic acid, Acetonitrile, Benzene, Toluene and Chloroform) fitted together based on the Connolly surface algorithm and the HF/6-31G* theory level using the R.E.D.-III program. Charges suitable for MD simulations using the Cornell et al. AMBER force field (and/or its different adaptations). Molecular orientation of the optimized structures controlled using the rigid-body reorientation algorithm implemented in R.E.D. (two or four mol. orientations for each structure).
Charge values identical (max. difference = +/- 0.0001, qtol = -5 in RESP) than those obtained in each project taken individually i. e. in the projects W-4, W-9, W-15, W-32, W-33, W-34, W-35, W-40, W-41 and W-42. Charge values to be compared with those reported in the projects W-47, W-48 and W-49.
Authors of the project
F.-Y. Dupradeau, A. Pigache, T. Zaffran, R. Lelong, N. Grivel & P. Cieplak

Is the project published NOT YET

"Whole molecule" or "Molecule fragment" type projectWHOLE MOLECULE

Interface R.E.D. used ? YES

Charge derivation procedure

Number of Tripos mol2 file(s) provided by the author(s) 10

Contain charge values & information about molecular topology

No	Name	Download	Wikipedia	3D visualization
1	Dimethylsulfoxide
2	Ethanol
3	Trifluoroethanol
4	Methanol
5	Acetone
6	Acetic acid
7	Acetonitrile
8	Benzene
9	Toluene
10	Chloroform

Number of molecule(s) used in the charge derivation procedure 10

File(s) provided to the PDB format

No	Molecule name	Conformation No	Reorientation procedure	Mol. orientation No
1	Dimethylsulfoxide	1	Rigid Body Reorient Algo	2
2	Ethanol	1	Rigid Body Reorient Algo	2
3	Trifluoroethanol	1	Rigid Body Reorient Algo	2
4	Methanol	1	Rigid Body Reorient Algo	2
5	Acetone	1	Rigid Body Reorient Algo	4
6	Acetic acid	1	Rigid Body Reorient Algo	4
7	Acetonitrile	1	Rigid Body Reorient Algo	2
8	Benzene	1	Rigid Body Reorient Algo	4
9	Toluene	1	Rigid Body Reorient Algo	4
10	Chloroform	1	Rigid Body Reorient Algo	2

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 CONNOLY 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...