Hi,
On Tuesday, March 11, 2014, Jason Swails <jason.swails.gmail.com> wrote:
>
> In this case, the only available option to fix your topology file is to
> use ParmEd. Since your solvent is not
Actually you could also use the 'solvent' command in cpptraj to define your
solvent followed by the 'parmwrite' command to write the correct topology.
-Dan
> water (let's assume that one of
> your solvent residues is named ION) you need to define your solvent to
> ParmEd first. So your parmed script should look something like below:
>
> === parmed.in ===
> parm your.prmtop
> defineSolvent :ION
> setMolecules solute_ions True
> parmout fixed.prmtop
> =================
>
> Then run ParmEd with the command
>
> parmed.py -i parmed.in
>
> The "fixed.prmtop" that it creates should be usable in sander and pmemd.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Mar 11 2014 - 06:00:02 PDT
