R.E.DD.B.: code F-65

Upload 11-04-2006 10:37 (Day-Month-Year, Paris time)

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

Firstname Julien

Lastname Pecher

Institute UFR de pharmacie, UPJV

City Amiens

Country FRANCE

General information about the Project

Molecule keywords

CYO

C3H4NO4S

Oxydized cysteine derivative

Sulfonate

Modified aminoacid

Abstract

RESP atomic charges for the central fragment of Sulfonate-L-cysteine, NHCHRCO [R = CH2SO3(-)]. Charges derived using N-Acetyl-sulfonate-L-cysteine-N'-methylamide (Single conformation close to that found in an alpha helix; dihedral constraints were used in the geometry optimization step to avoid intra-molecular hydrogen bonds and transition state type structures: phi = -60.0, psi = -40.0; single mol. orientation). Procedure automatically carried out using the R.E.D.-III program (mol. orientation generated by the QM program being conserved) 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). Charge values to be compared with those obtained for the project F-66.

Is the project published NOT YET

"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) 1

Contain charge values & information about molecular topology

No	Name	Download	Wikipedia	3D Display 1	3D Display 2
1	Central fragment of sulfonate-L-cysteine

Number of molecule(s) used in the charge derivation procedure 1

File(s) provided to the PDB format

No	Molecule name	Conformation No	Reorientation procedure	Mol. orientation No	Download	Wikipedia
1	Sulfonate-L-cysteine dipeptide	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...