Great, I’ll test and let you know the result.
Thanks!!
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
> On 19 Oct 2015, at 6:24 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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 <mailto: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> <
>> 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
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> http://lists.ambermd.org/mailman/listinfo/amber <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 - 09:00:03 PDT
