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

[Yegor Isakov]

this was not observed as I attached the similar chain
to a C atom

--- Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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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