I'm using Amber 16.0.
Thanks for your suggestions and advice Bill and Dan. Using cpptraj, I was
able to get the pdb file.
-Vatsal
On Mon, Feb 27, 2017 at 1:23 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> What version of AmberTools are you using?
>
> On Mon, Feb 27, 2017 at 12:52 PM, Vatsal Purohit
> <vatsal.purohit15.gmail.com> wrote:
> > 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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> >>
> >>
> >>
> >> --
> >> -------------------------
> >> 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
> >>
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>
>
>
> --
> -------------------------
> 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
>
> _______________________________________________
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Received on Mon Feb 27 2017 - 11:00:03 PST
