If you are looking for the equilibrium water distribution in the pocket you
can try using 3D-RISM to solvate the system. Tutorial here:
http://dansindhikara.com/Tutorials/Entries/2012/1/1_Using_3D-RISM_and_PLACEVENT.html
.
It would be useful not only to look at the placed waters but the 3D-RISM
distribution in the active site after the
calculation is done.
-Dan
On Wed, Dec 5, 2012 at 2:00 AM, Chris Chris <alpharecept.yahoo.com> wrote:
> Keep in mind that some enzymes have 'lids' that close to keep water
> molecules out of the active site during catalysis as the presence of water
> can lead to side reactions, see: www.pnas.orgcgidoi10.1073pnas.0408930102.
> This may not apply to you.
>
>
> ________________________________
> From: Zhenquan Hu <zhenquanhu.yahoo.com.cn>
> To: amber.ambermd.org
> Sent: Tuesday, December 4, 2012 8:42 AM
> Subject: [AMBER] problem in solvation of binding pocket
>
> Dear all,
>
> I tried to solvate my protein-ligand complex in tleap and found that there
> is a quite big empty space in the binding pocket. The reason is the pocket
> is quite huge while the ligand is rather small, even after equilibrium the
> space is still empty. I just wondering is it common that solvation method
> is not so good for AMBER to treat inner pocket?
>
> Regards,
> Zhenquan Hu
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--
Dr. Daniel J. Sindhikara <http://www.dansindhikara.com/Information.html>
Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
sindhikara.gmail.com <http://www.dansindhikara.com>
--
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Received on Tue Dec 04 2012 - 14:30:03 PST
