Hi Prof Luo,
Thank you very much for your helpful and informative reply.
If I understand correctly, by default:
ÄGrepulsive = molecular_volume*ã + c, where ã is the surface tension and c is the cavity offset, correct? How is the volume computed? More precisely, what volume is being used - solvent accessible (SAV) or solvent excluded volume (SEV)?
As for the keywords in the output:
EPB = ÄGelectrostatic
ENPOLAR = ÄGattractive (ÄGdispersion)
ECAVITY = ÄGrepulsive(ÄGcavitation)
and
ÄGnonpolar = ENPOLAR + ECAVITY
Finally,
ÄGsolvation = ÄGnonpolar + EPB
Is this correct?
Best wishes,
Stefan
________________________________________
From: Ray Luo [rluo.uci.edu]
Sent: Sunday, March 13, 2016 4:21 AM
To: AMBER Mailing List
Subject: Re: [AMBER] How is ÄGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist)
Hi Stefan,
> I would like to ask a few questions regarding MMPBSA.py's
> implementation in AMBER14. Having read the AMBER14 manual, the
> MMPBSA.py paper, and a few papers referenced in the manual, I'm a
> bit confused and unsure about a few things.
>
> What is the default scheme for computing ÄGsolvation in MMPBSA.py
> in AMBER 14 (default is inp = 2, according to the AMBER14 manual)?
> I'm specifically talking about the Poisson-Boltzmann computations, i.e.
> inp=2 in the &pb namelist (which is equivalent to not specifying
> anything for inp, because 2 is the default value, right)?. I think the
> manual is a bit unclear. From what I understand
This is correct.
> ÄGsolvation = ÄGelectrostatic + ÄGnonpolar
>
> and
>
> ÄGnonpolar = ÄGrepulsive(ÄGcavitation) + ÄGattractive (ÄGdispersion).
Yes, this is correct.
> Finally:
>
> ÄGrepulsive = ã*SASA + c
The default behavior is that the repulsive free energy is modeled as
linearly depended on the volume within SASA since this is the best
observed scheme for the tested small molecules and side chain mutation
data.
> where SASA is computed with the LCPO method. Is this correct or is
> the cavitation term proportional to molecular volume? If so, how is that
> computed?
If you choose to model it as linearly dependent on SASA, PBSA would
compute SASA numerically, it does not use the approximated LCPO
method.
> Here is a typical output file I get (see below). I see EPB, ENPOLAR,
> EDISPER, but no ECAVITY term. Does this mean that ENPOLAR is
> the (repulsive) cavitation term and EDISPER is the (attractive)
> dispersion term (although in this case ENPOLAR is negative and
> ECAVITY is positive)?
This is because the the printing of ECAVITY (inp=2) shares the same
routine as the printing ENPOLAR (inp=1) in the script. Again this is
because they both use linearly functional models. The sander printout
is more informative.
> Also, is the internal PBSA solver in sander linear or nonlinear?
It's linear by default.
> I have seen a lot of recommendations for the "perl" version of
> MMPBSA, but very little for MMPBSA.py. What settings would you
> recommend for doing Poisson-Boltzmann calculations on protein -
> protein complexes?
The two scripts should give you the same results if you use the same
options. The difference is that the perl script uses sander, and the
python script uses nab by default. If you prefer, you can use the
sander option in the python script so you can choose all the &pb
keywords as described in the manual. Apparently it is too hard to
support all &pb keywords in either scripts.
You may want to use inp=1 for protein-protein complexes because the
inp=2 was not optimized for macromolecular "ligand" binding, though we
are working on it.
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
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Received on Sun Mar 13 2016 - 19:30:03 PDT
