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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Received on Tue Dec 04 2012 - 09:30:03 PST
