On Tue, Nov 2, 2010 at 10:28 AM, Lekpa Duukori <duukori.gmail.com> wrote:
> You can use strip :WAT command in ptraj after reading in your topology and
> rst files.
>
> You may also need to use stripwaters command in rdparm to create a new
> topology file without the waters.
>
In my experience, sander will not work with a prmtop generated this way
since ptraj's output-prmtop is not the same version type as what amber uses
now (amber7 parm). It might work in pmemd since it has a different design
philosophy, but I've never tested it.
In any case, it may be easier to just use tleap to create a dry prmtop file
(but you WILL need to create one if you plan to use that restart to run
another simulation, or even just visualize). If you choose this route, you
can have ptraj output the file as a PDB (trajout file.pdb pdb)
Good luck!
Jason
>
> Lekpa
>
> On Tue, Nov 2, 2010 at 9:21 AM, Baptiste Legrand <bap.legrand.gmail.com
> >wrote:
>
> > Dear all,
> >
> > How can I delete the solvent molecules (eg water or chloroform) from my
> > rst files at the end of the refinement in a solvent box step. Thanks.
> >
> > Best wishes,
> > Baptiste
> >
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> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Nov 02 2010 - 09:30:03 PDT
