I’m using MMPBSA.py.MPI to calculate binding energies. The script I’m using is:
Input file for running PB and GB
&general
interval=2, endframe=10000, verbose=1,
# entropy=1,
/
&gb
igb=1, saltcon=0.100
/
&pb
inp=1, istrng=0.100,
/
Using inp=1 throws out warning messages indicating that inp=1 is the old default
Running the same calculation with inp=2 and comparing the results the discrepancies for the Poisson Bolzmann binding energies are pretty huge
GENERALIZED BORN (inp=1) -22.3955 kcal/mol -22.7632 kcal/mol (Complex - Receptor - Ligand)
POISSON BOLTZMANN (inp=1) -18.7747 kcal/mol 0.8206 kcal/mol (Complex - Receptor - Ligand)
I’d appreciate any suggestions regarding the differences in the results.
Thanks in advance
George
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Received on Wed Sep 17 2014 - 11:00:02 PDT
