[Chimera-users] Local execution of pdb2pqr and APBS

Conrad Huang conrad at cgl.ucsf.edu
Mon Dec 16 09:51:08 PST 2013

Ah.  Well.  Ermmm.

It's not possible right now due to an oversight on my part.  Although 
the functionality was all implemented, there is no way to invoke it. 
I've added some code to the command lines for apbs, pdb2pqr and vina. 
There are now three additional optional arguments to those commands:

- backend = "opal" | "local"
- service = Opal service name | path to executable
- url = Opal URL | unused

So a command like:

apbs backend local service /tmp/myapbs

should initiate a local computation process.  I say "should" because 
I've not installed APBS on my machine and am a little too busy to do it 
today.  However, when I test the above command, it does tell me that 
/tmp/myapbs is not an executable file, so the code at least somewhat 
works.  I thought I'd make that available in the daily build for 
tomorrow and let someone "volunteer" to test it. :-)   If you do have a 
chance to test it, please let me know whether it works.  I'll install 
and test it with apbs on my machine in the next couple days in any case.


On 12/16/2013 6:05 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
> Hi Chimera friends,
> Sorry to bother you again with so many questions.
> I'm trying to use PDB2PQR and APBS in a script to calculate an EP
> map. I know how to specify a local executable location for these
> external applications if I use the graphics interface, but the
> documentation that I can find does not indicate how to do this via
> the command line. Is it possible? How do I do it?
> Thanks! Darrell
> -- Darrell Hurt, Ph.D. Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
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