Thanks for your suggestion Dan. Unfortunately, I got the error 'unknown
flag: -c' when I tried that.
-Vatsal
On Mon, Feb 27, 2017 at 12:40 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Likely your restart file is in NetCDF format. Use the '-c' flag
> instead of a redirect, e.g.
>
> $AMBERHOME/bin/ambpdb -p complex.top -c complex-init-md.rst >
> complex-init-md.pdb
>
> Hope this helps,
>
> -Dan
>
> On Mon, Feb 27, 2017 at 12:29 PM, Vatsal Purohit
> <vatsal.purohit15.gmail.com> wrote:
> > Hello all,
> >
> > I am trying to convert an rst file to pdb after running a short md
> > simulation and am getting the following error:
> >
> > ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 11374 0\
> >
> > I used the following program:
> > $AMBERHOME/bin/ambpdb -p complex.top < complex-init-md.rst >
> > complex-init-md.pdb
> >
> > and my .out file after the simulation looks fine so I'm not sure what's
> > wrong with the rst.
> >
> > Kindly, advise.
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Feb 27 2017 - 10:00:02 PST
