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

From: Jacopo Sgrignani <>
Date: Wed, 28 Dec 2011 17:25:54 +0100

Dear Jiyuan
MCPB is reasonable, the second method in my opinion is very
unsatisfactory (and wrong), actually it does not conserve the X-ray
There are a lot of literature about metalloproteins simulations maybe
you can read L.Banci Curr Opin Chem Biol. 2003 Feb;7(1):143-9.

But the are also other interesting, and more recent review. However
also in this work of the 2003 there are some still valid lessons to
simulate metallo-proteins.


2011/12/28 JiYuan Liu <>:
> 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
> --
> 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
> _______________________________________________
> AMBER mailing list

Jacopo Sgrignani PhD
CNR-IOM-Democritos National Simulation Center
c/o International School for Advanced Studies (SISSA/ISAS)
via Bonomea 265,
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Received on Wed Dec 28 2011 - 08:30:02 PST
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