Deal All!
I test my system with MM-GBSA and MM-PBSA both:
################################################
&general
startframe=3641,endframe=4000, verbose=1,
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.15,radiopt=0,
/
&decomp
idecomp=1, print_res="1-252"
dec_verbose=0,
/
#############################################
and I use "set default PBRadii mbondi2" to prepare my prmtop file.
All goes well, and result belows:
GBSA:
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS 9.1993 4.5697 0.2408
EEL -903.7460 17.4715 0.9208
EGB 916.3956 14.1794 0.7473
ESURF -2.3127 0.0888 0.0047
DELTA G gas -894.5467 15.4122 0.8123
DELTA G solv 914.0829 14.1770 0.7472
DELTA TOTAL 19.5362 4.2174 0.2223
---------------------------------------------------------------------------------------
PBSA:
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS 9.1993 4.5697 0.2408
EEL -903.7460 17.4715 0.9208
EPB 868.5417 13.0425 0.6874
ENPOLAR -11.2088 0.4629 0.0244
EDISPER 19.7992 0.6073 0.0320
DELTA G gas -894.5467 15.4122 0.8123
DELTA G solv 877.1321 13.0279 0.6866
DELTA TOTAL -17.4146 7.8453 0.4135
We can see delta G of GBSA is 19.5362, where PBSA is -17.4146 and can be considered as a reasonable result for me.
The polar interaction is dominant where EGB is 916.3956 and EPB is 868.5417 making the result become a positive and negative delta G, respectively.
Obviously, GBSA overestimated the EGB, I want to know how can I do modification to parameter files to make GBSA's result become negative and reasonable??
PS: I have tried IGB=5, but still the same
Hope for your help.
Chirs
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 18 2015 - 03:00:02 PDT
