On Tue, Sep 13, 2011 at 7:48 PM, Rajesh Raju <rajesh.raju.mail.chem.tamu.edu
> wrote:
> Dear AMBER users,
>
> I have done mmpbsa binding free energy calculations on a 10-mer DNA
> structures using MMPBSA.py script. The MMGBSA binding free energy
> value changes from -43 kcal mol-1 to -60 kcal mol when included the
> saltcon parameter (saltcon=0.1). But the MMPBSA value doesnt show any
> significant change. only about ~0.5-0.7 kcal mol-1. what is the
> actural role of the saltcon as we are neutrilzaing the system before
> we do simulation..?
>
The saltcon is a debye screening parameter which theoretically approximates
the electrostatic screening induced by counterions. Explicit neutralizing
ions should *NOT* be included in implicit solvent calculations unless they
are functional and you do it very carefully. The formula for GB is found in
the Amber manual, I think, and also explicitly in the references cited in
the Amber manual (I remember a particularly good one by Bashford and Case,
IIRC, and Onufriev has some good ones out there, too).
For PB, try using the non-linear equation and see how that affects your
results. Note that GB's treatment of nucleic acid electrostatics are highly
suspect. NAs are highly charged systems, and GB has known problems when
used on them. I would suggest searching the literature for how others
approached similar problems.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Sep 13 2011 - 18:00:03 PDT
