Along the same lines, iIs there any chance I can get track of that surface
areas calculated by that approach? I know it is possible to calculate
residue based SASA through surf command of cpptraj module but I would love
to be able to compare ICOSA vs LCPO results.
Thanks,
Best,
Nihal Korkmaz
On Wed, Jun 27, 2012 at 4:14 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Jun 27, 2012 at 4:39 PM, E. Nihal Korkmaz
> <enihalkorkmaz.gmail.com>wrote:
>
> > Dear all,
> >
> > I am trying to run MMPBSA.py for my trajectory (explicit solvent) with
> this
> > input parameters here:
> > Input file for running GB
> >
> > &general
> > keep_files=2,
> > verbose=2,
> > interval=10,
> > strip_mask=":Cl-:Na+:WAT",
> > /
> > &gb
> > igb=5,
> > gbsa=2,
> > saltcon=0.2,
> > /
> >
>
> When we started using NAB to write the energy calculation routines (so that
> most of the functionality of MMPBSA.py could be wrapped up completely in
> the open-source AmberTools release), we dropped support for the "gbsa"
> variable directly in the MMPBSA.py input file, since NAB only supports the
> LCPO (gbsa=1) surface area method.
>
> If you really want to use the ICOSA approximation (gbsa=2), you will need
> to use sander (so put use_sander=1 in the &general section), then use
> --write-mdins, edit your mdin files to set gbsa=2, then re-run with
> --use-mdins to use these new values.
>
> The gbsa=2 option is necessary for residue decomposition, and so it is used
> by default when decomp is turned on.
>
> There should be little difference between gbsa=1 and gbsa=2 for MMPBSA.py
> binding free energies or stability free energies, so I would suggest just
> using the default unless you have a good reason to do otherwise.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644
Email: korkmaz.wisc.edu
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Received on Tue Aug 21 2012 - 21:30:02 PDT
