Dear Jason,
Thanks for the information. The cpptraj command worked.
But the problem is that, when I am using this newly prepared rst7 file as
an input coordinate (-c average.rst7), sander giving the following
error-------------
| peek_ewald_inpcrd: Box info not found in inpcrd
What should I do now ?
Dear Kenneth, I have already tried as you recommended and it worked.
Thanks
----indrajit
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
On Fri, Jun 5, 2015 at 9:19 PM, Kenneth Huang <kennethneltharion.gmail.com>
wrote:
> Indrajit,
>
> VMD should be able to save the pdb as a rst file- I'm not sure if amber has
> that utility, or if there's other options. Alternatively, you could just
> use your average pdb as an input in tleap to make a new topology and
> coordinate file to run in sander.
>
> Best,
>
> Kenneth
>
> On Fri, Jun 5, 2015 at 11:26 AM, Indrajit Deb <biky2004indra.gmail.com>
> wrote:
>
> > Dear amber users,
> >
> > I have a average pdb file which have short contacts. I want to convert
> the
> > average pdb file into rst file, so that I can use it as an input for
> > sander. Actually I want to energy minimize the average pdb.
> >
> > So how to convert average pdb file into rst file ?
> >
> > Thanks
> >
> > ----indrajit
> >
> >
> >
> >
> > ---------------------------------------------------------------------
> > Indrajit Deb
> > Kolkata, India.
> > Mob: +919239202278
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
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> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
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Received on Fri Jun 05 2015 - 10:00:02 PDT
