VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 20 2012 - 15:57:24 CDT

Erik,
  I'm going to reply to both of your emails on this topic so the other
APBS users can see it as well. To answer your question, so long as you
can get the atom coordinates, charge, and radii information into VMD
by some method either by loading files or by using atom selections to
set/update/override these data fields, then you should be able to
perform APBS jobs on each such configuration. The APBS plugin distributed
with VMD was written primarily for graphical use, however I believe that
you could probably override the GUI inputs and call its internal routines
directly without too much difficulty. If you have a look at the code for
the APBS plugin, you can see the different GUI routines, and then the
worker routines that generate the output files and run the APBS job.
If the only thing you're changing with each run is the molecular structure
data, then I believe you may be able to get away with calling the
::APBSRun::apbs_start routine after each update to your molecular
structure data. You might have to call other routines for each structure
if there are significant changes in the molecules, but I would start by
setting up the APBS job in the GUI, and then running your own script to
launch multiple invocations of ::APBSRun::apbs_start instead of clicking the
GUI run/start button.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 07, 2012 at 09:41:54AM -0500, Martin, Erik W wrote:
> Hi, the APBS feature in VMD appears to take either .psf paramterized or amber prmtop files as inputs and write the .pqr file needed for APBS calculation. This is remarkably easy for a single calculation, but I'm looking to automate calculations on a trajectory or every structure in an ensemble. I was wondering if this feature (converting a namd or amber parameterized file to .pqr) is available to the command line for scripting? Of for that matter, if any of the APBS functionality in VMD is available via the command line?
>
> Thanks,
> Erik
>
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