On Tue, Sep 13, 2011 at 8:59 PM, Rajesh Raju <rajesh.raju.mail.chem.tamu.edu
> wrote:
> Hi Jasaon,
>
> Thanks for ur kind reply...I could not find an option in AMBERTOOL
> manual for setting up 'non-linear' equation..How to do non-linear PB
> calculation...? Wat I have that when I included the saltcon=0.1, the
> MMGBSA value becomes close to MMPBSA..
>
You actually need to look at the PBSA section of the manual. I think nbpopt
is the variable controlling which type of PB solution you get (npbopt=2, I
think). Then what you have to do is use the -make-mdins flag to create a
bunch of mdin files. Find the _MMPBSA_pb.mdin file, modify npbopt to be 2,
then re-run MMPBSA.py with the -use-mdins flag. That will force non-linear
PB. I'll let others comment on caveats here if there are any (I haven't
done this myself).
HTH,
Jason
> Thanks
> Rajesh
>
> On Tue, 13 Sep 2011 20:43:17 -0400
> Jason Swails <jason.swails.gmail.com> wrote:
> > 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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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 Sep 13 2011 - 20:30:03 PDT
