yes,
I used the bond command in tleap.
On Tue, Sep 28, 2010 at 4:29 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> are you sure you defined the disulfide bond in leap? it isn't automatic.
>
>
> On Tue, Sep 28, 2010 at 6:55 AM, <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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
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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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Received on Tue Sep 28 2010 - 05:00:04 PDT
