(unknown charset) [AMBER] Which methodology could estimate the binding affinity of zinc containing metalloprotei(wrong string) 每ligand complex accurately?

From: (unknown charset) JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Fri, 30 Mar 2012 23:00:35 +0800

Hi,

I encountered a problem for the calculation of binding affinity with
zinc containing metalloprotein-ligand complex,I used MCPB to handle with
my metalloprotein每ligand complex,after 26ns MD course,the conformation
of the metal center included the ligand was very conserved the X-ray
structure.I selected MMPBSA to calculate the delta G for the
complex,however the value of std.dev was so big especially vdwaals of
the ligand,if I deleted the coordination bonds in the prmtops of
"complex" and "receptor",the std.dev changed into smaller than before.

My question is:

1. Whether I deleted the coordination bonds in the prmtops of "complex"
and "receptor" for perform MMPBSA calculation is reasonable?
2.Except MMPBSA,which methods could predict the binding affinity
correlation with experiment so well for metalloprotein-ligand complex?

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


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Received on Fri Mar 30 2012 - 08:30:02 PDT
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