On Wed, Aug 22, 2012 at 12:19 AM, E. Nihal Korkmaz
<enihalkorkmaz.gmail.com>wrote:
> 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.
>
Actually cpptraj doesn't support ICOSA, just LCPO and molsurf SAs. You can
use the energy dump (-eo flag in MMPBSA.py) along with the suggestion I
provided below to compare LCPO and ICOSA surface areas.
HTH,
Jason
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Aug 21 2012 - 22:00:03 PDT
