Re: [AMBER] MMPBSA final results of MMPBSA.py different fromtutorial

From: Ray Luo <rluo.uci.edu>
Date: Sun, 22 May 2016 08:47:15 -0700

Yes indeed, this is because of the different inp choices and or
different scaling factors used for the nonpolar solvation term.

The tutorial pages regarding this will be updated to include more
information regarding nonpolar solvent models and discuss the
different choices.

All the best,
Ray

--
Ray Luo, Ph.D.
Professor
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Sat, May 21, 2016 at 10:01 AM, David A Case <david.case.rutgers.edu> wrote:
> On Sat, May 21, 2016, LI An-Bang wrote:
>
>> I compared my results with that on the tutorial page.
>> (http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm )
>>
>> only the nonpolar part of the PB results are different.
>
>> The nonpolar parts in my results are shown with components "ENPOLAR" and "EDISPER",
>> while the nonpolar parts on the webpage are shown only with "ECAVITY".
>
> OK...the way in which nonpolar components of PBSA are done by default has
> changed over the years--others on the list can give more details here.  Look
> at the value of the "inp" variable: it may be different in your run than in
> the one on the tutorial -- it's very easy for tutorials to get out of date.
>
> ....dac
>
>
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Received on Sun May 22 2016 - 09:00:02 PDT