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
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>
--
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 - 08:30:06 PDT
