Dear all, I am trying to calculate the binding energy of a protein ligand
complex using MMPBSA from AmberTools 1.5. I find that while the GB results are
almost same for both MMPBSA and MMPBSA.MPI there is significant difference in in
PB values. I am using 25 processors for MMPBSA.MPI. I am using the exact same
script for both. I found a similar problem in archives and thus applied the
suggested patches. However I still have the problem. Here are the results:
MMPBSA:GB: Delta Total = -38.6156
PB: Delta Total = -50.4641
MMPBSA.MPI:GB: Delta Total = -36.4499
PB: Delta Total = -18.5299
I find that the main difference is arising due to G SOLV of ligand (-4.8 vs
-50.02).
Can someone please help me with this?
Amin.
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
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Received on Fri May 11 2012 - 03:00:05 PDT
