[AMBER] How to handle with two Zn2+ when calculates the free binding energy by mmpbsa.py in metalloprotein

From: JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Thu, 16 Feb 2012 21:56:11 +0800

Hi,

I have handled with the metalloprotein that includes two zn2+ in the
active site by MCPB successfully,and performed 12 ns MD for
equilibration and 20 ns for production.The plots density, temperature,
total energy and backbone RMSD looks so well.When I ran the command
"$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
-sp 1err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
ligand.prmtop -y *.mdcrd",I encountered a problem:Although I have
obtained the prmtop of complex and which is solvated,I don't know how to
deal with two zn2+ whether regard as receptor or ligand.And how could I
get the correct receptor.prmtop and ligand.prmtop.

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 Thu Feb 16 2012 - 06:00:04 PST