Hi Chen.
If you are up for it, pdb2pqr exist in the Pymol-script repo.
http://pymolwiki.org/index.php/Git
I have made a automatic compile script.
See here:
http://pymolwiki.org/index.php/User:Tlinnet/Linux_Install#Install_script
That should fix it for you.
Try to look it through, and just write if you have problems.
Troels Emtekær Linnet
2013/6/18 Chen Zhao <chenzhaoh...@gmail.com>
> I am using Debian linux and I installed PDB2PQR with path specified in
> pymol APBS GUI. However, it seems that there are some problems in python,
> although I don't understand because I am not a programmer. I will try to
> run from command line instead.
>
> Thank you!
>
> Chen
>
>
> On Tue, Jun 18, 2013 at 11:08 AM, Troels Emtekær Linnet <tlin...@gmail.com
> > wrote:
>
>> Do you have linux or windows?
>>
>> Do you have PDB2PQR on your system?
>> http://pymolwiki.org/index.php/Apbsplugin
>> http://www.poissonboltzmann.org/pdb2pqr
>>
>>
>> Troels Emtekær Linnet
>>
>>
>> 2013/6/18 Chen Zhao <chenzhaoh...@gmail.com>
>>
>>> Thank you so much Troels,
>>>
>>> This solves my problem. But based on this, it seems that APBS In pymol
>>> failed to find PDB2PQR.
>>>
>>> Chen
>>>
>>>
>>> On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet <
>>> tlin...@gmail.com> wrote:
>>>
>>>> Have a look on the earlier message on this.
>>>>
>>>>
>>>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html
>>>>
>>>>
>>>>
>>>> Troels Emtekær Linnet
>>>>
>>>>
>>>> 2013/6/18 Chen Zhao <chenzhaoh...@gmail.com>
>>>>
>>>>> 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/PmwBase.py",
>>>>> line 1747, in __call__
>>>>> return apply(self.func, args)
>>>>> File
>>>>> "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", 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/PmwDialog.py", line 132,
>>>>> in _doCommand
>>>>> return command(name)
>>>>> File
>>>>> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
>>>>> line
>>>>> 1075, in execute
>>>>> self.runPsize()
>>>>> File
>>>>> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
>>>>> line
>>>>> 1096, in runPsize
>>>>> good = self.generatePqrFile()
>>>>> File
>>>>> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
>>>>> line
>>>>> 1007, in generatePqrFile
>>>>> good = self._generatePdb2pqrPqrFile()
>>>>> File
>>>>> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
>>>>> 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
>>>>> apbs_tools.py file, the APBS GUI in pymol is still unable to show the
>>>>> correct path of APBS and PDB2PQR.
>>>>>
>>>>> Thank you so much!
>>>>>
>>>>> Sincerely,
>>>>> Chen
>>>>>
>>>>>
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>>>>
>>>>
>>>
>>
>
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