[AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW

From: JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Wed, 28 Dec 2011 22:58:01 +0800

Hi everyone,

3H68 is a metalloprotein that includes two ZN2+/MN2+,the ligand which is
a small molecule has dicarboxylic acid that be in ionization state in
the metal center.Metal M1 is coordinated by three ligand oxygens (by one
oxygen from each carboxylate moiety and by the furanic ring oxygen),
while metal M2 is coordinated by only one of the carboxylate oxygens,
which is bridging with M1.Now I used two methods to handle this
metalloprotein named 3H68,who could tell me which method is reasonable:

1. I used MCPB to handle the metal center includes the ligand of 3H68.

2. I only consider the Electrostatic and VDW in 3H68,the ligand is given
the RESP charge with it's value -2,two ZN2+ is used 2+ for it's
charge,and the protein used the GAFF,I have run 1 ns MD for 3H68 with
second method to solve the metal center included ligand,the result is
that two Zn2+ and ligand were so stable in the metal center,but the pose
of the ligand with metal center is changed worsely compare to the
crystal structure.

Best Regards

Jiyuan Liu
Key Laboratory of Plant Protection Resources and Pest Management,National Ministry of Education
Northwest A&F University
Yangling, Shaanxi
China 712100
Phone: 86-29-87092190
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Received on Wed Dec 28 2011 - 07:00:04 PST
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