[Chimera-users] huge electrostatic range for APBS

Tom Goddard goddard at sonic.net
Wed Aug 6 18:39:31 PDT 2014

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.


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-
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