Dear Users,
I am calculating binding free energy for protein-peptide complex. When I am
using inp=1 and radiopt=0, I am getting a large difference between delta G
for GB and PB calculations. While, if I am using inp=2, radiopt=0 (
http://archive.ambermd.org/201208/0089.html), I am getting PB bomb error
during MMPBSA.py run. Following are my input and corresponding outputs for
MMPBSA calculations-
*Input file for running PB and GB*
&general
startframe=1000, endframe=1400, interval=50,verbose=2,
entropy=1, strip_mask=:WAT:Na+,
/
&gb
igb=5, saltcon=0.150,
/
&pb
istrng=0.100,fillratio=4.0,
inp=1, radiopt=0,
/
*Corresponding output is- *
For GB section-
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 0.0000 0.0000
0.0000
ANGLE 0.0000 0.0001
0.0000
DIHED -0.0000 0.0000
0.0000
VDWAALS -110.1017 7.0312
1.5343
EEL -225.7126 19.0563
4.1584
1-4 VDW 0.0000 0.0001
0.0000
1-4 EEL 0.0000 0.0000
0.0000
EGB 295.7762 17.6341
3.8481
ESURF -14.2568 0.7890
0.1722
DELTA G gas -335.8143 21.0157
4.5860
DELTA G solv 281.5194 17.3843
3.7936
*DELTA TOTAL -54.2949 7.9276
1.7299*
and for PB section-
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 0.0000 0.0000
0.0000
ANGLE 0.0000 0.0001
0.0000
DIHED -0.0000 0.0000
0.0000
VDWAALS -110.1017 7.0312
1.5343
EEL -225.7126 19.0563
4.1584
1-4 VDW 0.0000 0.0001
0.0000
1-4 EEL 0.0000 0.0000
0.0000
EPB 273.6640 17.4261
3.8027
ENPOLAR 2342.0140 114.0742
24.8930
EDISPER 0.0000 0.0000
0.0000
DELTA G gas -335.8143 21.0157
4.5860
DELTA G solv 2615.6780 120.3178
26.2555
*DELTA TOTAL 2279.8638 108.7266
23.7261
*
Results of PB and GB section have very large difference. I will deeply
appreciate if someone help me to figure out this problem.
--
With best regards
*******************************************************************************************************************
Kshatresh Dutta Dubey
Post Doctoral Fellow
Indian Institute of Technology Kanpur
Kanpur, India
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Received on Tue May 14 2013 - 04:00:03 PDT
