What do you mean by they are "too large"?
On Dec 23, 2014 8:28 AM, "朱亚莉" <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 - 06:00:02 PST
