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.



On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming <moloch525@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.

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