Summary of information
PROJECT
Central fragment of S-methyl-L-cysteine

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Upload 11-04-2006 13:17 (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

CYM C4H7NOS Thio-methyl Cysteine derivative Modified aminoacid


Abstract

RESP atomic charges for the central fragment of S-methyl-L-cysteine, NHCHRCO (R = CH2SMe). Charges derived using N-Acetyl-S-methyl-L-cysteine-N'-methylamide (Two conformations close to those found in alpha helix and extended forms; phi = -75.46, psi = -30.51 and phi = -116.58, psi = 150.13; 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 B3LYP/cc-pVTZ theory level in diethylether: Polarized Continuum Model (PCM) using the Integral Equation Formalism (IEF). Charges suitable for MD simulations using the Duan et al. AMBER force field. Charge values to be compared with those obtained for the project F-69.

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 visualization
1 Central fragment of S-methyl-L-cysteine Link Wiki Logo Jmol Logo


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 S-methyl-L-cysteine dipeptide 2 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 DFT B3LYP

More information 2 IOp(6/33=2) SCRF(IEFPCM,Solvent=Ether)

Basis set 2 cc-pVTZ

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



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