Dear Carlos:
Thx for reply. A negative dG should explain favorable interaction between ligand and protein, so, I think, PBSA gives a reasonable approximate energy, althought -TdS is not included.
On the other hand, GBSA is more approximate, but, I think it SHOULD give a correct property of energy, a negative number. Because, positive and negative of energy represented
a totally different property of system.
What I am doubted is if I am using a improper parameters for GBSA calculation or just GBSA is not suitable for my system.
Yours sincerely
Chris
At 2015-06-18 20:05:11, "Carlos Simmerling" <carlos.simmerling.gmail.com> wrote:
>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 - 06:00:03 PDT
