On Mon, Feb 7, 2011 at 5:33 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> This because istrng is the unit of mM, while saltcon is the unit of M ...
> please set istrng = 150 and try again ...
>
MMPBSA.py takes input as M and then converts it to mM for PBSA internally
(to maintain consistency with GB), so setting istrng will write out 150000
as the ionic strength in the sander input file. (This is mentioned in the
MMPBSA.py manual for those that are using that). For mm_pbsa.pl I believe
you have to input the value as mM, though, so this is something to be
careful of.
All the best,
Jason
> Ray
>
> On Mon, Feb 7, 2011 at 1:14 PM, Robert Elder <rmelder.gmail.com> wrote:
>
> > Hi all,
> >
> > When I perform Poisson-Boltzmann calculations for MM-PBSA, I've noticed
> > that
> > the value of ionic strength has virtually no effect on the calculated
> > electrostatic contribution. The maximum change I've observed is ~2
> kcal/mol
> > between 0 and 150 mM. This is inconsistent with my intuition for the
> > system,
> > as well as Generalized Born calculations, which change by 10's of
> kcal/mol.
> > I've tried these calculations with both the mm_pbsa.pl and MMPBSA.py
> > scripts
> > to no avail. I'm using Amber 10 with all bug fixes applied (and all
> Python
> > script bug fixes applied). Here's a sample input for the Python script:
> >
> > MMPBSA.py:
> > &general
> > startframe=2000, endframe=10010, interval=120, keep_files=2, verbose=2,
> > /
> > &gb
> > igb=5, saltcon=0.150,
> > /
> > &pb
> > istrng=0.150
> > /
> >
> > Analyzing the verbose outputs, I cannot see any overt errors or warnings,
> > and the only difference I observe versus the zero ionic strength case is
> > that istrng/saltcon in the PB/GB .in files are changed to the appropriate
> > values (150 and 0.150, respectively).
> >
> > On changing ionic strength, the only individual contribution that changes
> > is
> > the E(GB) or E(PB), which of course is expected. Here's some sample
> output
> > of delta E(GB) and delta E(PB) for 0 mM and 150 mM:
> >
> > IS 0 mM:
> > E(GB): 8197
> > E(PB): 8208
> >
> > IS 150 mM:
> > E(GB): 8275
> > E(PB): 8206
> >
> > As you can see, the GB energy gets less favorable (expected) but the PB
> > energy stays the same. I've tried this with a variety of salt
> > concentrations
> > with no difference in behavior. I first observed this issue in some
> > somewhat
> > exotic systems, but I've had the same problem even when calculating the
> > energy of melting of DNA, i.e. this is force field independent. (The DNA
> > melting calculations were for testing purposes only; I know they aren't
> > reliable indicators of, say, relative melting temperatures.)
> >
> > I'm at a loss as to what I should do. Is it possible that I compiled
> Amber
> > without some important flag or additional program? Please let me know
> what
> > further details I can provide or where you think I should look.
> >
> > Best,
> >
> > Robert Elder
> > PhD Candidate
> > University of Colorado - Boulder
> > _______________________________________________
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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. Graduate Student
352-392-4032
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Received on Mon Feb 07 2011 - 15:00:09 PST
