[gmx-users] Re: CHARGES AN LJ14 PARAMETERS

[Marc A Ceruso]

Hi-

I need to build a palmitoylated cystein. The lipid group and the cysteine
are covalently linked via a thioester linkage. I am facing two different
problems:

    1- how to chose the charges on and near the thioester linkage:
R-CH2-CO-S-CH2-R'
    Has anyone described such a chemical group?

    2- If I use the lipid parameters (atom types and LJ) to describe the
palmitoyl moiety then I need to generate the LJ14 "pairs" parameters (since
they do not exist in the forcefieldand grompp assigns a value of zero for
the incriminated LJ14 interactions ). Does anyone know how the values of the
LJ14 parameters are generated?

Thanks for your help

marco
____________________________________________________________________________
____

    Department of Physiology & Biophysics
    Mt Sinai School of Medicine
    One Gustave L. Levy Place
    New York NY 10029

    Tel  : 212-241 82 93
    Fax  : 212-860 33 69
    mceruso at physbio.mssm.edu
____________________________________________________________________________
____





----- Original Message -----
From: "Pedro Alexandre de Araujo Gomes Lapido Loureiro"
<paloureiro at biof.ufrj.br>
To: <gmx-users at gromacs.org>
Sent: Thursday, May 16, 2002 10:01 AM
Subject: [gmx-users] Re: Charge groups II


Dear David and Anton,

I am simulating a DPPC bilayer with PME. When I use charge groups, the
program
halts due to LINCS violation. This problem was solved when I began to use
atom-based charges.
Has anybody experienced similar problems?

Cheers, Pedro.
--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil
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