On Tue, 28 Sep 2010 15:06:44 +0530
hirdesh kumar <hirdeshs8.gmail.com> wrote:
> Hi,
> But I don't know the how to check the connection between S-S in the
> minimized structure.
Write a restart file with 'ntwr' in your input file for minimisation and
then load it together with the topology file into vmd as I have
described in my previous email or with File->New Molecule... from the
menu. I guess pymol can do something similar.
> I *want to keep the S-S bond intact during minimization* so that it
> does not break. Is there any way for the same.
The AMBER force fields do not allow bonds to break. If the
disulfide bond is properly defined but you still get an unnatural
elongation then your problem is somewhere else.
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Received on Tue Sep 28 2010 - 03:00:06 PDT
