[AMBER] Positive MM-PBSA and negative MM-GBSA binding energies

From: Nada Afiva <nadaafiva.gmail.com>
Date: Fri, 26 Jun 2020 05:08:24 +0700

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
| startframe=0, endframe=10000, keep_files=2, interval=100,
| verbose=2,
| igb=5, saltcon=0.1,
| 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,
AMBER mailing list
Received on Thu Jun 25 2020 - 15:30:03 PDT
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