Dear list,
I am performing MM-PBSA and MM-GBSA binding energy calculation using input
file below.
However, I got final MM-GBSA=-23.15 kcal/mol, while MM-PBSA =+11.43 kcal/mol
I used single trajectory of MD, and obtained ligand and receptor topology
using Ante-MMPBSA.
Here is the input file:
Input file for running MMPBSA
|&general
| startframe=0, endframe=10000, keep_files=2, interval=100,
| verbose=2,
|/
|&gb
| igb=5, saltcon=0.1,
|/
|&pb
| istrng=0.1, exdi=80, indi=1.0,
inp=2, cavity_surften=0.0378, cavity_offset=-0.5692,
fillratio=4.00, scale=2.0
linit=1000, prbrad=1.4, radiopt=1,
|/
Thanks in advance.
Best regards,
nadaafiva
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Received on Thu Jun 25 2020 - 15:30:03 PDT
