How did you set up your system? If you used "solvateCap" command in LEap,
then the waters in the cap should move only within the sphere you defined.
Regards,
Junjun
On Tue, Mar 20, 2012 at 4:01 AM, Yi An <anyiphysics.gmail.com> wrote:
> Hi AMBER users,
>
> I'm working on a ligand-protein binding project and now I'm trying to
> simulate the ligand-protein complex in a solvatecap (the size of solvatecap
> is smaller than the size of protein). Is there any methods to restrain the
> water molecules so that they can just move within the cap? I tried the
> regular way (using RES and a force of 200kcal/mol*square angstrom) but the
> waters still drifted away...Thank you in advance.
>
> Yi An
> Graduate student
> Chemistry Department
> Texas A&M university
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Received on Mon Mar 19 2012 - 21:00:02 PDT
