AMBER Archive (2005)

Subject: Re: AMBER: Is the MD simulation normal

From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Thu Jun 30 2005 - 10:00:11 CDT

Prof. Walker Ross,

I also perform a MD on a protein- ligand complex whose ligand was
docked to the active site. The similar problem arises.

As you said, if the docked ligand is used, the position may be off
and so the ligand would rapidly change orientation and move away from
the peptide. If this happens, what does it mean? Does it mean the
docking reuslt is not right? My docking result is in agreement with
one paper.But no MD study was performed on this ligand.

If the problem is casued by the weak binding affinities of the ligand
or the docking ligand, How should I do?

best regards 

-- 
   Shulin Zhuang
Chemistry Department 
Zhejiang University PRC
shulin.zhuang_at_gmail.com
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