Dear all,
I was interested in carrying out MM PBSA analysis of a protein with a set
of ligands.
My output file is as follows:
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
| endframe=1000, verbose=2,
| full_traj=1,
| interval=5,
| netcdf=1,
| entropy=0,
|/
|&gb
| igb=5, saltcon=0.100,
|/
|&pb
| istrng=0.100,
| inp=1,
| radiopt=0,
|/
GB
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
DELTA G gas -42.3091 2.3895
0.1690
DELTA G solv 10.5381 1.0797
0.0763
DELTA TOTAL -31.7710 2.3820
0.1684
PB
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
DELTA G gas -42.3091 2.3895
0.1690
DELTA G solv 24.9932 1.7929
0.1268
DELTA TOTAL -17.3158 2.7028
0.1911
The difference between the PB and GB calculations seems to be high. Could
someone please tell me, if this is normal and what this difference means.
P.S: the calculation performed on the other ligand (with the same input
files) yielded a better result. PB calculation being -5 less than GB
calculation.
--
Regards,
Prasanth.
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Received on Fri Apr 19 2019 - 06:30:03 PDT
