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 - 07:00:09 PDT
