I have the same problems. If you use the pymol pqr grid instead of the pdb2pqr,
you will find that it works.
Sent from my iPhone
On Aug 8, 2012, at 6:24 PM, Warren Gallin <wgal...@ualberta.ca> wrote:
> Hi,
>
> I am trying to generate some electrostatic surfaces using the APB plugin,
> but I am getting the following error message when I click on the Set Grid
> button.
>
>
> --------------------------
> PDB2PQR - a Python-based structural conversion utility
> --------------------------
> Please cite your use of PDB2PQR as:
> Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
> PDB2PQR: an automated pipeline for the setup, execution,
> and analysis of Poisson-Boltzmann electrostatics calculations.
> Nucleic Acids Research 32 W665-W667 (2004).
>
> Exception raised by main.mainCommand!
> (<type 'exceptions.UnboundLocalError'>, UnboundLocalError("local variable
> 'bestangle' referenced before assignment",), <traceback object at
> 0x112f28ef0>)
> In show error 2
> Could not generate PDB2PQR file. _generatePdb2pqrPqrFile failed.
> Could not generate PQR file!
>
> I am a Mac PowerBook, running Mountain Lion OSX 10.8.
>
> I am running PyMol as PyMOLX11Hybrid.app so I can use the plugins. I have
> downloaded the latest versions APBS and PDB2PQR and copied apbs, prize.py and
> pdb2pqr.py into the default free mol locations inside the application, and I
> am using the 1.5.0.4 prebuilt incentive version of PyMol.
>
> Any suggestions as to how to pursue and fix this problem?
>
> Thanks,
>
> Warren Gallin
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threat landscape has changed and how IT managers can respond. Discussions
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threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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