Hi,
I think the output file is ok. Here I am attaching the file also.
On Tue, Sep 28, 2010 at 4:25 PM, <steinbrt.rci.rutgers.edu> wrote:
> 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.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks and Regards,
Hirdesh,
******************************************
Hirdesh Kumar
PhD Scholar
School of Biological Sciences
Indian Institute of Technology, Delhi
Hauz Khaas, New Delhi-16
http://www.iitd.ac.in/bioschool.html
******************************************
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- application/octet-stream attachment: min1.out
Received on Tue Sep 28 2010 - 04:30:03 PDT
