The energy difference you mentioned (-44.23 vs. -67.1321) is comparing two
different models: The -44.23 comes from using the GB implicit model and
-67.1321 comes from running the PB implicit model. This large of a
difference is fairly common between GB and PB since GB is really just a
cheap approximation of PB. If you look at the two PB models, they are
actually relatively close (-63.39 from mm_pbsa.pl and -67.1321 from
MMPBSA.py). Several of the default values in MMPBSA.py are different from
the suggested values in mm_pbsa.pl, and those differences probably account
for the small difference seen in MM-PBSA results. See the manual for the
default values for the input files.
I hope that helps.
-Bill
2010/8/12 pxq <pangxueqintea.yahoo.com.cn>
> Dear Jason,
>
> Thank you for your replay. Then if I do not calculate entropy then it
> is ok with this temperature difference.
>
> Another problem is, my calculation stop when doing mm_pbsa for the
> ligand (because of the traj of this snapshot), is it possible for me to
> restart the calculation? As you know calculation for complex and receptor is
> really time consuming.
>
> A third problem I am facing now is the result form mm_pbsa.pl and
> mmpbsa_py difference a lot some part of my snapshots ( -44.23 vs. -67.1321).
> Attach is my input and output for both of them. Do you have any ideas why
> this happens?
>
> If further information is needed please e-mail me.
>
> Thanks again for you kind help
>
> Xueqin
>
>
>
>
>
>
> ======= 2010-08-11 23:03:06 您在来信中写道：=======
>
> >Hello,
> >
> >I believe that the only part of the calculation that really uses the
> >temperature are the entropy calculations. You can see that the
> temperature
> >is defined in mm_pbsa_statistics.pm, and you can change it there (look
> for
> >TEMP). However, take care if you're looking to change the temperature for
> >entropy calculations, as the temperature 298.15 is hard-coded into the
> >source codes of both nmode and nab. Therefore, changing the temperature
> >requires you to change the default value in every location that uses the
> >temperature and then recompiling the corresponding programs that you
> >changed, then re-running the mm_pbsa simulations. There may be pieces
> here
> >that I'm missing, but I think I got the important ones.
> >
> >Hope this helps,
> >Jason
> >
> >2010/8/10 pxq <pangxueqintea.yahoo.com.cn>
> >
> >> Hello everyone,
> >>
> >> I am using mm_pbsa.pl to calculate the binding free energy between
> >> the ligand and protein. But the given temperature of mm_pbsa.pl is 300K
> >> while my simulation temperature is 310K, is it ok to use 300K to
> calculate?
> >> If not, how to change temperature in the input script? Cause there is no
> >> such option so far as I know.
> >>
> >> Thanks ahead for your kind help
> >>
> >> Xueqin
> >>
> >>
> >>
> >>
> >>
> =============================================================================================================
> >> Pang Xueqin
> >> State Key Laboratory of Molecular Reaction Dynamics
> >> Dalian Institute of Chemical Physics
> >> Chinese Academy of Sciences.
> >> Tel: 0411-84379352
> >> Mobile: 15840973721
> >> Fax: 0411-84675584
> >> E-mail: pxq.dicp.ac.cn
> >> http://english.dicp.cas.cn/
> >>
> >>
> =============================================================================================================
> >>
> >> __________________________________________________
> >> 赶快注册雅虎超大容量免费邮箱?
> >> http://cn.mail.yahoo.com
> >>
> >>
> >> _______________________________________________
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> >>
> >
> >
> >
> >--
> >Jason M. Swails
> >Quantum Theory Project,
> >University of Florida
> >Ph.D. Graduate Student
> >352-392-4032
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
> = = = = = = = = = = = = = = = = = = = =
>
>
> 致
> 礼！
>
>
> pxq
> pangxueqintea.yahoo.com.cn
> 2010-08-12
>
>
> _______________________________________________
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>
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Thu Aug 12 2010 - 08:30:12 PDT
