someone else have done this structure before.
the DELTA G gas is expected to be -100kcal/mole ~0.
the DELTA G solv is expected to be 0~100kcal/mole.
yzhu
At 2014-12-23 21:31:45, "Carlos Simmerling" <carlos.simmerling.gmail.com> wrote:
>What do you mean by they are "too large"?
>On Dec 23, 2014 8:28 AM, "ÖìÑÇÀò" <zhuyalitj.gmail.com> wrote:
>
>> Hi,
>> I do a MM-GBSA calculation to calculate the binding free energy of
>> AChE-HI6,and the PDB ID is 2GYU. As for the structure, I only do a short
>> minimization before MM-GBSA calculation. In the minimization, only H
>> atoms are allowed to move.But the strange things are DELTA G gas and
>> DELTA G solv are too large. What's wrong?
>>
>> Differences (Complex - Receptor - Ligand):
>> Energy Component Average Std. Dev. Std. Err.
>> of Mean
>>
>> -------------------------------------------------------------------------------
>> VDWAALS -29.3676 0.0000 0.0000
>> EEL -518.5458 0.0000 0.0000
>> EGB 526.4798 0.0000 0.0000
>> ESURF -5.7166 0.0000 0.0000
>>
>> DELTA G gas -547.9134 0.0000 0.0000
>> DELTA G solv 520.7632 0.0000 0.0000
>>
>>
>> DELTA G binding = -27.1502 +/- 0.0000 0.0000
>>
>> my input file is
>>
>> #INPUT
>> | &general
>> | endframe=1,verbose=1,strip_mdcrd=0,
>> | /
>> | &gb
>> | igb=2,saltcon=0,
>> | /
>>
>> thanks,
>> Zhu
>>
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Received on Tue Dec 23 2014 - 19:00:02 PST
