[AMBER] The value of Delta G is positive after MMPBSA calculation for metalloprotein

From: JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Wed, 14 Mar 2012 11:02:24 +0800

Hi,

The active pocket of my metalloprotein contains two zinc ions,my ligand
is coordinated with these two zinc ions,so I used MCPB to handle with
them,and obtained the force filed and charge information for the metal
center.Before I performed the MMPBSA calculation,I have performed the
below MD simulation: heat 500ps;density 500ps;equil 5ns;production
20ns.I checked the plot of the density, temperature, total energy and
backbone RMSD during the heat,the density,and the equilibration,The
density, temperature,total energy,and backbone RMSD plots have all
clearly converged by the end of our equilibration period.In production
period those plots as well as the three in the above.Then I constructed
three prmtops:
complex_solvate.prmtop,complex.prmtop,receptor.prmtop,ligand.prmtop,specially
the receptor.prmtop includes two zinc ions.Although everything looked so
well,the value of Delta G is positive after MMPBSA calculation.I sent
mmpbsa.in and the FINAL_RESULTS_MMPBSA.dat in the attachment.Please help
me,thanks a lot.

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 Tue Mar 13 2012 - 20:30:04 PDT
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