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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jan 29 2013 - 09:30:03 PST
