[gmx-users] Re: two negtively charhed atoms blow out my molecule

[Tsjerk Wassenaar]

Hi Yegor,

Are you sure that the negative charges on the *-S-(C=O)-* are the cause of
the trouble? The S and O should be interacting through bonded terms, notably
the angle, and not be influenced by the charges. 1-3 interactions
(nonbonded) are by default excluded. Was your starting structure reasonable
and did you perform energy minimization?Did grompp give any warnings?

Cheers,

Tsjerk

On 2/8/06, Yegor Isakov <yegoris at yahoo.com> wrote:
>
>
>
> --- Yegor Isakov <yegoris at yahoo.com> wrote:
>
> > I appresiate help from anybody.
> > I have designed myself topology for a molecule where
> > cysteine  is connected to another chain through
> > carbonyl group
> > (oneChain-S-CO-anotherChain). Negative electrostatic
> > charges on S and O atoms blow out my molecule within
> > several cycles. grompp.mdp file contains more or
> > less
> > general parameters I used in previous simulation of
> > proteins.
> > Thanks in advance.
> > Yegor
> >
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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