[AMBER] controversy in PBSA and GBSA results

From: <h_sahakyan.mb.sci.am>
Date: Wed, 30 Sep 2020 11:42:30 +0000

Dear All,

I used MM-PBSA/GBSA methods to calculate the binding free energy between two subunits of a protein. The binding energies were -101 and -94 kcal/mol for GBSA and PBSA respectively. However, in the presents of a ligand (between two subunits), binding energies were -124/-67 (GBSA/PBSA). As you can see, according to GBSA the ligand makes the interaction stronger and vice versa according to the PBSA calculation. What can be the reason for this controversy?

I used MMPBSA.py with following input:

 startframe=1, interval=50, endframe=5000,
 verbose=2, keep_files=0, netcdf=0,
 strip_mask = ":WAT,Cl-,Na+,K+,",
 ligand_mask = ":1-437,867,869",
 receptor_mask = ":438-865,866,868,870",
inp=1 # I tried inp=2 it gives more weird results, generally with positive energy values
Best wishes,
Senior Assistant at Laboratory of
Computational Modeling of Biological Processes,
Institute of Molecular Biology, NAS RA
7 Hasratyan St, Yerevan, Armenia
Tel: +374 93 323990
E-mail: h_sahakyan.mb.sci.am (mailto:h_sahakyan.mb.sci.am)
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Received on Wed Sep 30 2020 - 05:00:03 PDT
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