Hi Andreas.

The line:

shows that you are using the apbs tools from Michael G. Lerner.

You might want to try out a little modified version of that.

You might also want to try this.
That is the repository with all scripts from Pymolwiki, to work out of the box.

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2013/1/3 Andreas Förster <docandreas@gmail.com>
Dear all,

on our RHEL computers (6.2, 64-bit) with PyMOL compiled from CVS, the
APBS2 plugin isn't functioning anymore.  The plugin window opens just
fine and the executables are found.

When I select "Use PDB2PQR" in the Main tab, clicking on Set grid
produces the following error:

Error: 1
<type 'exceptions.UnboundLocalError'> Exception in Tk callback
   Function: <function <lambda> at 0x7fc2b0705410> (type: <type 'function'>)
   Args: ()
Traceback (innermost last):
   File "/usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py",
line 1747, in __call__
     return apply(self.func, args)
"/usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwDialog.py", line
153, in <lambda>
     command=lambda self=self, name=name: self._doCommand(name))
"/usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwDialog.py", line
132, in _doCommand
     return command(name)
"/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py", line
1075, in execute
"/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py", line
1096, in runPsize
     good = self.generatePqrFile()
"/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py", line
1007, in generatePqrFile
     good = self._generatePdb2pqrPqrFile()
"/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py", line
1615, in _generatePdb2pqrPqrFile
     if retval != 0:
<type 'exceptions.UnboundLocalError'>: local variable 'retval'
referenced before assignment

When I chose "User PyMOL generated PQR and PyMOL generated Hydrogens and
termini" or "User PyMOL generated PQR and existing hydrogens and
termini", I can set the grid, run APBS and visualize the result just fine.

I'm happy with that, but maybe someone has an idea of why the first
approach fails.



         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London

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