That's because in the time between when the tutorial was written and the
current version of the code, the default nonpolar solvation model changed,
unfortunately. If you compare the *polar* solvation free energy component
(EPB), you *should* find that they are very similar.
Indeed, if you compare them, the tutorial lists 57.6402 kcal/mol as the
polar solvation free energy of binding, while your output gives 56.7534
kcal/mol. I don't know why the discrepancy is as large as 1.1 kcal/mol,
but it's certainly a lot smaller than 35 kcal/mol.
If you want to recover the original tutorial results (or values close to
it), set radiopt=0 and inp=1 in your &pb section and try again. I really
should try to find some time to update the tutorial...
Hope this helps,
Jason
On Mon, Oct 19, 2015 at 10:17 AM, Fabian gmail <fabian.glaser.gmail.com>
wrote:
> Dear Amber colleagues,
>
> I am doing all the MMPBSA tutorials, and I found consistently that while
> the GENERALISED BORN results are almost identical to the tutorial (using
> the tutorial .mdrcd and .prmtop files) the POISSON BOLTZMANN results are
> completely different. As I said I only did the MMPBSA.py calculation, using
> given files. For example using the following command for tutorial files A
> 3.2 (
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm <
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm>)
> I got the following FINAL_RESULTS_MMPBSA.dat file, which as you see for
> the POISSON BOLTZMANN yields a much lower DELTA TOTAL -6.6887 compared to
> the tutorial DELTA G binding = -41.7256 !!
>
> Why is that?????
>
> As explained above the GENERALISED BORN results are much more similar, for
> my calculation is DELTA TOTAL -52.3853 and the tutorial is
> DELTA G binding = -52.2672. That is great.
>
> I used the command and input files provided on the tutorial:
>
> MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> 1err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> ligand.prmtop -y *.mdcrd
>
> I want to test this method on several systems, so it’s important for me to
> understand the differences…. any hint will really help me. The same happens
> on 3.1 so I suspect there is something different or wrong with the
> calculation.
>
> Thanks a lot in advance,
>
> Fabian
>
> ____________________
> Dr. Fabian Glaser
>
> Head of the Structural Bioinformatics section
>
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
> Engineering
> Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
>
> fglaser at technion dot ac dot il
> Tel: +972 4 8293701
> http://bku.technion.ac.il
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Oct 19 2015 - 08:30:05 PDT
