Thanks Jason,
It worked.
On Tue, Jan 29, 2013 at 5:59 PM, Jason Swails <jason.swails.gmail.com>wrote:
> You have to use cpptraj, not ptraj.
>
> ParmEd will also generate stripped topologies.
>
> Good luck,
> Jason
>
> On Tue, Jan 29, 2013 at 11:20 AM, HM <scienceamber.gmail.com> wrote:
>
> > Hi All,
> > I am using following script to strip water and Na+ ions from my file:
> >
> > parm complex_wat.prmtop
> > parmstrip :WAT
> > parmstrip :Na+
> > parmwrite out complex_nowat.prmtop
> >
> > and I am geting following error:
> >
> >
> > WARNING in dispatchToken: Token string "parm" not found in tokenlist
> >
> >
> > WARNING in dispatchToken: Token string "complex_wat.prmtop" not found in
> > tokenlist
> >
> >
> > PTRAJ: parmstrip :WAT
> >
> > WARNING in dispatchToken: Token string "parmstrip" not found in tokenlist
> >
> >
> > WARNING in dispatchToken: Token string ":wat" not found in tokenlist
> >
> >
> > PTRAJ: parmstrip :Na+
> >
> > WARNING in dispatchToken: Token string "parmstrip" not found in tokenlist
> >
> >
> > WARNING in dispatchToken: Token string ":na+" not found in tokenlist
> >
> >
> > PTRAJ: parmwrite out complex_nowat.prmtop
> >
> > WARNING in dispatchToken: Token string "parmwrite" not found in tokenlist
> >
> >
> > WARNING in dispatchToken: Token string "out" not found in tokenlist
> >
> >
> > WARNING in dispatchToken: Token string "complex_nowat.prmtop" not found
> in
> > tokenlist
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 30 2013 - 06:30:03 PST
