Hi,
also, check if your minimization has insanely high vdw clashes at step 0,
either ********* or some ~7 digit number. This would indicate that leap
did not form the SS bond as planned.
Thomas
On Tue, September 28, 2010 5:51 am, Hannes Loeffler wrote:
> 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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>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Sep 28 2010 - 04:00:04 PDT
