Dear All
I am trying to do MM-PBSA calculation for determining binding energy for the complex of receptor and an small ligand. I went through the MMBPSA tutorial and used python-based version of MM-PBSA. Unfortunately PB did not work, I ignored the PB and continued with GB. After calculation the delta G was -4124.0239. The question is that is this energy of binding for a complex of small molecule and a receptor reasonable and why the PB did not work. The result was as follows:
FINAL_RESULTS_MMPBSA.dat Run on Mon Oct 3 04:32:16 2016||Input file:|--------------------------------------------------------------|Input file for running PB and GB|&general| endframe=1000, verbose=1,|# entropy=1,|/|&gb| igb=2, saltcon=0.100|/|#&pb| istrng=0.100, |/|--------------------------------------------------------------|MMPBSA.py Version=14.0|Solvated complex topology file: ao-lig-min_solvated.prmtop|Complex topology file: ao-ami.prmtop|Receptor topology file: ao.prmtop|Ligand topology file: ami.prmtop|Initial mdcrd(s): prod10-10.mdcrd||Receptor mask: ":1-1333"|Ligand mask: ":1334"|Ligand residue name is "ami"||Calculations performed using 1000 complex frames.||Generalized Born ESURF calculated using 'LCPO' surface areas||All units are reported in kcal/mole.--------------------------------------------------------------------------------------------------------------------------------------------------------------
GENERALIZED BORN:
WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIALTERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
...Your help in this regard would be highly appreciated.
All the bestMaryam
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Received on Mon Oct 03 2016 - 00:00:02 PDT
