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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Received on Wed Jun 27 2012 - 14:30:02 PDT
