Hi,
Which version of PyMOL, APBS and PDB2PQR are you using?
If you send me a PQR file off-list, I can take a closer look at what's going
on.
Thanks,
-Michael
On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming <moloch...@gmail.com> wrote:
> Hi all,
>
> I've been trying to get APBS Tools and/or APBSTools2 running for a
> few weeks now on multiple linux systems (RedHat and Fedora). I've
> Installed MALOC and APBS Tools. I can start up Pymol through Phenix,
> load a .pqr generated from a PDB2PQR server, start APBS Tools, set the
> grid, but when I click on Run APBS I get: "ObjectMapLoadDXFile-Error:
> Unable to open file!"
>
> If I use the "pymol generated PQR" option with my .pqr even though
> it is a PDB2PQR server generated file APBS runs and states "X atoms
> did not have properties assigned" and to either remove or fix the
> atoms. How can I fix them? The "problem" residues are just regular
> amino acids; no split confrimations etc. I've also tried editing out
> the PDBs chain name before converting to the PDB to PQR but that
> didn't work.
>
> Another things I've tried is using APBSTools 2 but it errors as soon
> as I click "set grid" with: Error: 2 ... Attribute Error: elec_radius.
>
> I really need to get this to work but I have no clue what to try next.
>
> Thanks in advance for any thoughts.
> -Jon
>
>
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--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
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Bethesda MD 20892-9314 (USPS)
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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