This because istrng is the unit of mM, while saltcon is the unit of M ...
please set istrng = 150 and try again ...
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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Received on Mon Feb 07 2011 - 15:00:07 PST
