I'm sorry to make you confused. What I meant is in this
tutorial(
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm),
they set saltcon=0.100 and istrng =0.100, which made me think the default
is 0.100. Thanks for the reply.
Yi
On Apr 19, 2011 10:09am, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
> On Tue, Apr 19, 2011 at 8:02 AM, anyiphysics.gmail.com> wrote:
> > Hi AMBER users,
> >
> > I noticed for python and perl versions of MMPBSA, they have different
> > default input values of 'saltcon' and 'istrng'.
> >
> > The python version sets saltcon=0.100 and istrng =0.100 while the perl
> > version sets saltcon and istrng equal to zero.
> >
> This is not true. MMPBSA.py also sets saltcon=0.0 and istrng=0.0 by
> default. The only way you can get non-zero ionic strength is by setting
> these variables in the input file. The manual says this as well. Where did
> you get this conflicting information? (Since I would like to make sure
> that's consistent everywhere)
> > My questions are: 1. Since we already added some counterions to
> neutralize
> > the system in the beginning, is it still necessary to set saltcon and
> > istrng equal to some number here?
> >
> Yes. Explicit neutralizing counterions should not be used in MM/PBSA
> analysis. Salt concentrations are accounted for via a Debye screening
> parameter (and, indeed, that's the Boltzmann- part of Poisson-Boltzmann).
> The only ions you should consider keeping are buried ions critical to
> binding.
> 2. The different values will result in different binding energies, right?
> >
> Yes, but "how" different will depend on your system. However, salt
> concentration changes the PB/GB potential energy term.
> HTH,
> Jason
> >
> > Thanks for your reply in advance.
> >
> > Yi An
> > Graduate Student
> > Department of Chemistry
> > Texas A&M University
> > _______________________________________________
> > 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 Apr 19 2011 - 09:30:02 PDT
