On Wed, Feb 5, 2014 at 10:01 PM, Yip Yew Mun <yipy0005.gmail.com> wrote:
> Hi, I wish to ask if it's possible to specify a fixed number of water
> molecules when solvating a protein molecule? Thanks.
>
I assume you mean in tleap. The answer is no -- this is not possible. The
best you can do is make your solvent buffer large enough so that you have
almost the exact number of water molecules you want (try to get as close to
your target value as possible). Then you can use ParmEd or cpptraj to
strip out the extra water molecules you don't want to reach your target
value.
An alternative is to use packmol to build your system.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Feb 05 2014 - 20:00:02 PST
