Dear jason.swails,
I have received your reply, thank you very much. However, I have still no well-known about reply.First, What is the meaning about
"The ipb = 1 method is basically the same as the simple SASA model used in GB." ? And how to understand the ipb=1 ? Next,in your reply,
you write "If you used the nonploar model in PB that is closer to what the GB model is doing your results would be much closer." , I wanted to know how to alter parameter to achieve this goal.
Thanks again.
Qiankun Gong
> -----原始邮件-----
> 发件人: "Jason Swails" <jason.swails.gmail.com>
> 发送时间: 2018-08-15 10:20:33 (星期三)
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] MMPBSA.PY
>
>
>
> > On Aug 12, 2018, at 10:37 PM, 龚乾坤 <m201770109.hust.edu.cn> wrote:
> >
> > Dear amber users and developers,
> >
> > I used mmpbsa.py to calculate binding free energy about protein, but I have some questions about the produce and result.
> >
> > Firstly,what is the mean about ENPOLAR and EDISPER in PB RESULT. Secondly, there is a huge difference in PB AND GB.
>
> ENPOLAR is the nonpolar solvation free energy contribution — a repulsive term proportional to the surface area of the molecule.
>
> EDISPER is a dispersion term that is attractive and, again, proportional to the surface area of the molecule. Together, the sun of these two terms are analogous to the ESURF term in GB. The ipb = 1 method is basically the same as the simple SASA model used in GB.
>
> >
> > How to account for it? Following is my result and input file:
> >
> >
> >
> >
> > &general
> > startfram=1000, endframe=1002, interval=1,
> > /
> > &gb
> > igb=2, surften=0.005, surfoff=0.0
> > /
> > &pb
> > exdi=80.0, indi=1.0,
> > /
> >
> >
> >
> >
> > GB RESULT
> >
> > Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of Mean
> > -------------------------------------------------------------------------------
> > VDWAALS -75.6534 2.2141 1.2783
> > EEL -145.1634 9.2722 5.3533
> > EGB 174.4558 6.1140 3.5299
> > ESURF -6.2697 0.1965 0.1134
> >
> > DELTA G gas -220.8168 7.4953 4.3274
> > DELTA G solv 168.1861 6.1991 3.5790
> >
> > DELTA TOTAL -52.6307 1.2974 0.7490
> >
> >
> >
> >
> > PB RESULT
> >
> > Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of Mean
> > -------------------------------------------------------------------------------
> > VDWAALS -75.6534 2.2141 1.2783
> > EEL -145.1634 9.2722 5.3533
> > EPB 161.1728 6.3935 3.6913
> > ENPOLAR -50.7773 1.6444 0.9494
> > EDISPER 96.1218 1.6736 0.9663
> > DELTA G gas -220.8168 7.4953 4.3274
> > DELTA G solv 206.5173 5.7788 3.3364
> > DELTA TOTAL -14.2995 1.7223 0.9944
> >
> >
> > Thank you in advance
>
> Notice that the bulk of the difference here stems from the contributions to the ESURF vs. ENPOLAR + EDISPER terms. If you used the nonploar model in PB that is closer to what the GB model is doing your results would be much closer.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Fri Aug 17 2018 - 00:30:03 PDT
