Alternatively, you can use parmed
parmed -i parmed.in
your parmed.in file:
parm your_topology.parm7
loadRestrt your_coord.rst7
summary
strip :tot_water-1316-tot_water
summary
outparm new_topology.parm7 new_coord.rst7
summary shows how many solvent molecules you have (sanity check)
On Fri, May 17, 2019 at 10:19 AM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Dear Elena,
>
> There is no way to do it with tleap... use cppptraj instead... check on
> the command "strip", you will then have to save the updated coord and
> topology...
>
> Best,
>
> MatÃas
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [pasteur.uy/en/labs/biomolecular-simulations-laboratory/]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Elena Gomez" <elengr93.hotmail.com>
> Para: amber.ambermd.org
> Enviados: Viernes, 17 de Mayo 2019 5:09:35
> Asunto: [AMBER] Selecting number of waters in tleap
>
> Hello Amber Users:
>
> I'm trying to do a targeted molecular dynamics but i'm having several
> difficuties. When i run my scripts an error appears: NATOM mismatch in
> coord and topology files. I fuigured out this happens because of the number
> of waters but, how can I "select" in tleap the number of waters with which
> I want to solvate the systems? I wouldn't want to remove them manually
> because there are 1317 water residues of difference between the systems.
>
> Thank you.
>
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--
Kellon A. A. Belfon, Graduate Student
Carlos Simmerling Laboratory
The Laufer Center for Physical and Quantitative Biology
The Department of Chemistry, Stony Brook University
Stony Brook, New York 11794
Phone: (347) 546-4237 <(347)+546+4237> Email: kellon.belfon.stonybrook.
<kellon.belfon.stonybrook.edu>edu
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Received on Fri May 17 2019 - 11:30:02 PDT
