Hi Amber Community
I have found some problems with the use the mmpbsa with my molecule. I'm
trying to evaluate the PBTOT, GBTOT of these ligand into specific protein
receptor. I have the experimental values of
inhibition of these molecules and trying to find a theoretical reasons
for the observed experimental values, a correlation between them. I did the
minimization, heating and equilibration steps, plus two
nanoseconds of production step. I checked the mdcrd file in VMD at each
step. And no change in the protein structure was found. After
the extraction of snapshots, I calculated energy using MMPBSA.pl. The
internal energy and the van der Waal energy of ligand was very high .Then i
checked the one of the extracted snapshot of ligand in the VMD. The ligand
went distortion during extraction.
Please help me out.
Thanks for your suggestions.
--
Nitu Bansal
M.S Pharm III Sem
Research Scholar
Department of Pharmacoinformatics
S.A.S Nagar NIPER Mohali (Chandigarh)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 22 2011 - 09:00:04 PST
