I used same input prm files as tutorial to repeat the tutorial calculation. the input parameter file is as following:
&general
endframe=50, keep_files=2,
/
&gb
igb=2, saltcon=0.100,
/
&pb
radiopt=0, istrng=0.100, inp=1, cavity_surften=0.00542, cavity_offset=-1.008
/
then I got the following value:
All unit is kcal/mol
tutorial
me
GB
PB
GB
PB
VDWAALA
-56.2934
-56.2934
-56.2921
-56.2921
EEL
-38.0300
-38.0300
-38.0301
-38.0301
EGB/EPB
EGB: 50.2053
EPB: 57.6402
EGB: 50.2050
EPB: 56.8405
DELTA G non-polar
-8.1491
-5.0423
-8.2682
-5.0423
DELTA G gas
-94.3234
-94.3234
-94.3222
-94.3222
DELTA G solv
42.0562
52.5978
41.9369
51.7982
DELTA G binding
-52.2672
-41.7256
-52.3853
-42.5240
My EPB value is very different from that of tutorial. I really do not know which parameter can cause their difference. Many years past, mmpbsa.py updated the default parameter and maybe the computational method.
Therefore, can you help me to find the reason causing the different value of me and tutuorail.
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Received on Fri Aug 26 2022 - 21:30:03 PDT
