Dear everyone,
I am using MMPBSA.py to compute the binding affinity of a protein-ligand
system. My input file is:
input file for running PB and GB
&general
endframe=20, keep_files=2,
/
&gb
igb=2,saltcon=0.100
/
&pb
istrng=0.100,
/
However, the calculated results are very strange, with the deltaG=
4.73kal/mol:
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -39.1172 3.1360
0.7012
EEL -64.1091 4.9433
1.1054
EPB 83.7146 6.2319
1.3935
ENPOLAR -29.2044 0.8518
0.1905
EDISPER 53.4513 1.2155
0.2718
DELTA G gas -103.2263 5.7924
1.2952
DELTA G solv 107.9616 6.5209
1.4581
DELTA TOTAL 4.7353 5.7145
1.2778
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Then I add a option in the &pb session of the input file: inp=1, (the
default is inp=2), then the results is much better:
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS -39.1172 3.1360
0.7012
EEL -64.1091 4.9433
1.1054
EPB 83.7146 6.2319
1.3935
ENPOLAR -3.9779 0.1122
0.0251
EDISPER 0.0000 0.0000
0.0000
DELTA G gas -103.2263 5.7924
1.2952
DELTA G solv 79.7368 6.1816
1.3822
DELTA TOTAL -23.4895 5.3000
1.1851
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
I checked the manual, and found that inp=1 or inp=2 just mean that
MMPBSA.py using different methods to calculate the non-polar term of
solvation energy. So, is the large difference between these results are
normal? Or did I make some thing wrong?
Please help me to figure it out!
Thank you so much!
Tong
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Received on Fri Apr 04 2014 - 08:30:09 PDT
