Chris,
If PB works well (although it's not clear to me how you have determined
that the PB result is "better"), why try to use GB? For what you are doing
I usually prefer PB. GB is more approximate but faster so it has the
advantage for use during md, but not for post-processing.
Note also that there is a significant difference in these 2 calculations I
your nonpolar solvation result.
You might look into the literature for what options people use with gb for
doing mm-gbsa validated against experiment, for example work by Rob Rizzo.
On Jun 18, 2015 5:33 AM, "Chris" <dlutlife223.163.com> wrote:
> 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
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Received on Thu Jun 18 2015 - 05:30:03 PDT
