[Chimera-users] huge electrostatic range for APBS

Dennis N Bromley dbromley at uw.edu
Wed Aug 6 20:19:19 PDT 2014


thank you Tom, this is great.  It gives me something to work with.  Another
part of my question is why two structures of the same protein would give
such dramatically different ranges.  Is it again due to some local
structural feature where one protein has a surface that allows close access
to a charged atom and the other doesn't?  But that doesn't make much
physical sense unless the surface calculation is doing something funny...?


On Wed, Aug 6, 2014 at 6:39 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Dennis,
>
>   The “Set full range” button when coloring the molecular surface using
> APBS electrostatic potential values is looking at the minimum and maximum
> potential values on the surface (actually 1.4 Angstroms out from the
> surface).  Your question is why do you observe such high values with the
> APBS potential, while the Chimera Coulomb potential never seems to give
> high values.  The high potential values are at points very close to charged
> atoms.  Why would that happen in the APBS case?  One thought is that the
> APBS calculation included water or ion charges while the Coulomb
> calculation did not, and those ions were close to the surface and the 1.4
> Angstrom offset from the surface ended up measuring the potential right on
> top of an ion.
>
>   In any case using the “set full range” button is not very sensible in
> this situation because it sets the coloring range using the most extreme
> values which are outliers.  But it is good you tried it since it seems to
> suggest something is perhaps wrong with APBS calculation, or at least
> somehow potential values are being used at points that are unexpectedly
> close to charged atoms.
>
>         Tom
>
>
> On Aug 6, 2014, at 3:13 PM, Dennis N Bromley  wrote:
>
> > Hi all,
> >
> > I have two proteins models from different points in an MD simulation.  I
> colored the surface by Coulombic Surface Coloring, which ran AnteChamber
> and such.  Then I ran APBS.  When I color by the APBS data, they look more
> or less similar.  But when I click the "Set full range" button, the kBTe
> unit range on one is about +-3 and the unit range on the other is about
> +-300.  Any ideas why one would be so much larger?  Or am I misinterpreting
> something?  Both were run with exactly the same parameters, all default
> except for temperature = 310.
> >
> > thanks-
> > -denny-
> >
> >
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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