Great thanks!
Only one more thing, I am trying to compile the MPI version on my MAC of MMPBSA.py.MPI, but despite I follow your instructions…. it fails:
==> sudo port install python27 py27-tkinter py27-mpi4py py27-matplotlib
---> Computing dependencies for python27
---> Cleaning python27
---> Computing dependencies for py27-tkinter
---> Cleaning py27-tkinter
---> Computing dependencies for py27-mpi4py
---> Cleaning py27-mpi4py
---> Computing dependencies for py27-matplotlib
---> Cleaning py27-matplotlib
---> Scanning binaries for linking errors
---> No broken files found.
==> MMPBSA.py.MPI
Traceback (most recent call last):
File "/Users/admin/Data/TOOLS/amber14/bin/MMPBSA.py.MPI", line 51, in <module>
raise MMPBSA_Error('Could not import mpi4py package! Use serial version '
MMPBSA_mods.exceptions.MMPBSA_Error: Could not import mpi4py package! Use serial version or install mpi4py.
I compiled it several times.
Thanks a lot,
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 20 Oct 2015, at 4:59 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Tue, Oct 20, 2015 at 8:41 AM, Fabian gmail <fabian.glaser.gmail.com>
> wrote:
>
>> Hi Again,
>>
>> Still getting one warning….
>>
>> Beginning GB calculations with
>> /Users/admin/Data/TOOLS/amber14/bin/mmpbsa_py_energy
>> calculating complex contribution...
>> calculating receptor contribution...
>> calculating ligand contribution...
>>
>> Beginning PB calculations with
>> /Users/admin/Data/TOOLS/amber14/bin/mmpbsa_py_energy
>> calculating complex contribution...
>> Warning: inp=1 was old default
>> Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
>> value: 1.400
>> calculating receptor contribution...
>> Warning: inp=1 was old default
>> Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
>> value: 1.400
>> calculating ligand contribution...
>> Warning: inp=1 was old default
>> Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
>> value: 1.400
>>
>
> This is just telling you that it's changing the default SASA probe radius
> from 0.557 to 1.4, which is the suitable default for the inp=1 nonpolar
> solvation model (compared to 0.557, which is the suitable default for the
> inp=2 nonpolar solvation model). In these cases, the warnings are telling
> you that the inp=2 defaults are being replaced by the *old* inp=1 defaults,
> which is what you *want* to happen when using inp=1 instead of inp=2 :).
>
>
>
>>
>> And the final PB energy… different from tutorial
>>
>> DELTA TOTAL -43.9050 2.8684
>> 0.4056
>>
>> parameters I used this time following, are there correct?
>>
>
> "Correct" depends on your system. Do not focus all of your energy on
> reproducing the tutorial results exactly -- it merely demonstrates how to
> run the software. The results were generated probably ~4 years ago, and
> much has changed in the PB solvers since then.
>
> Rather than focusing on exactly reproducing the tutorial results here,
> focus on learning how to run MMPBSA.py (which it seems that you have), and
> then spend that time and effort researching what PB settings you should be
> using in this version of Amber (based on recent literature).
> Unfortunately, I have not followed recent developments closely enough to
> make the best suggestions. Because of that, I would probably just switch
> to the defaults I *was* comfortable and familiar with (inp=1 with the old
> surface tension and offset), since I knew roughly how well that model
> performed.
>
> In the meantime, hopefully we can get the tutorial updated to eliminate
> this confusion in the future!
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Oct 20 2015 - 07:30:04 PDT
