Do you have linux or windows?

Do you have PDB2PQR on your system?

Troels Emtekær Linnet

2013/6/18 Chen Zhao <>
Thank you so much Troels,

This solves my problem. But based on this, it seems that APBS In pymol failed to find PDB2PQR.


On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet <> wrote:
Have a look on the earlier message on this.

Troels Emtekær Linnet

2013/6/18 Chen Zhao <>
Dear Pymol Users,

I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian Wheezy machine. The initialization is successful, but when I hit "set grid", I got the error message below:

error: 1
<type 'exceptions.UnboundLocalError'> Exception in Tk callback
  Function: <function <lambda> at 0x33a6938> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/", line 1747, in __call__
    return apply(self.func, args)
  File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/", line 153, in <lambda>
    command=lambda self=self, name=name: self._doCommand(name))
  File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/", line 132, in _doCommand
    return command(name)
  File "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/", line 1075, in execute
  File "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/", line 1096, in runPsize
    good = self.generatePqrFile()
  File "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/", line 1007, in generatePqrFile
    good = self._generatePdb2pqrPqrFile()
  File "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/", line 1615, in _generatePdb2pqrPqrFile
    if retval != 0:
<type 'exceptions.UnboundLocalError'>: local variable 'retval' referenced before assignment

Also, although I specified the PATH of APBS and PDB2PQR in file, the APBS GUI in pymol is still unable to show the correct path of APBS and PDB2PQR.

Thank you so much!


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