On Tue, Aug 6, 2013 at 6:39 AM, Andre C. Stiel <andre.stiel.tuebingen.mpg.de
> wrote:
> Hi,
>
> I use the "closest" command in ptraj to delete all solvent except near
> some important residues (mask).
> How do I change my .prmtop using parmed.py accordingly, because with
> "strip" in parmed I have to exactly specify the waters that have been
> stripped. Do I have to read them out manually somehow or is there a more
> convenient way.
>
Dan's way is the easiest way to output a compatible prmtop. You can still
do it with ParmEd -- just realize that all of the water molecules are
indistinguishable. Therefore, if you keep the 50 closest waters using the
closest command, make sure you strip all but the first 50 waters from your
prmtop. (This is actually all that cpptraj does under the hood).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 06 2013 - 12:00:03 PDT
