Hi,
I do a MM-GBSA calculation to calculate the binding free energy of
AChE-HI6,and the PDB ID is 2GYU. As for the structure, I only do a short
minimization before MM-GBSA calculation. In the minimization, only H
atoms are allowed to move.But the strange things are DELTA G gas and
DELTA G solv are too large. What's wrong?
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -29.3676 0.0000 0.0000
EEL -518.5458 0.0000 0.0000
EGB 526.4798 0.0000 0.0000
ESURF -5.7166 0.0000 0.0000
DELTA G gas -547.9134 0.0000 0.0000
DELTA G solv 520.7632 0.0000 0.0000
DELTA G binding = -27.1502 +/- 0.0000 0.0000
my input file is
#INPUT
| &general
| endframe=1,verbose=1,strip_mdcrd=0,
| /
| &gb
| igb=2,saltcon=0,
| /
thanks,
Zhu
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Received on Tue Dec 23 2014 - 05:30:02 PST
