Dear amber users and developers,
I used mmpbsa.py to calculate binding free energy about protein, but I have some questions about the produce and result.
Firstly,what is the mean about ENPOLAR and EDISPER in PB RESULT. Secondly, there is a huge difference in PB AND GB.
How to account for it? Following is my result and input file:
&general
startfram=1000, endframe=1002, interval=1,
/
&gb
igb=2, surften=0.005, surfoff=0.0
/
&pb
exdi=80.0, indi=1.0,
/
GB RESULT
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -75.6534 2.2141 1.2783
EEL -145.1634 9.2722 5.3533
EGB 174.4558 6.1140 3.5299
ESURF -6.2697 0.1965 0.1134
DELTA G gas -220.8168 7.4953 4.3274
DELTA G solv 168.1861 6.1991 3.5790
DELTA TOTAL -52.6307 1.2974 0.7490
PB RESULT
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -75.6534 2.2141 1.2783
EEL -145.1634 9.2722 5.3533
EPB 161.1728 6.3935 3.6913
ENPOLAR -50.7773 1.6444 0.9494
EDISPER 96.1218 1.6736 0.9663
DELTA G gas -220.8168 7.4953 4.3274
DELTA G solv 206.5173 5.7788 3.3364
DELTA TOTAL -14.2995 1.7223 0.9944
Thank you in advance
Qiankun Gong
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Aug 12 2018 - 20:00:03 PDT
