Hi Christian.

I had a similar problem on my windows machine, but with .
Try to set the temp path.

fetch 4ins, async=0

import os
print os.environ['temp']
print os.getcwd()
and then run the apbs plugin.

My own problem on my windows computer, was that I default had set .py files to be opened with
notepad++. When I in apbs plugin then executed the "Set grid", the pdb2pqr would be opened in Notepad++
instead of executing the script.
I had to default opening of .py files to python before it worked.

I dont know if these problems would be meaning full on CentOS ?

Please report how it goes :-)

Troels Emtekśr Linnet
Ved klÝvermarken 9, 1.th
2300 KÝbenhavn S
+45 60210234

2012/9/27 Christian Roth <christian.roth@bbz.uni-leipzig.de>
Dear all,

we have with our system Ubuntu a problem with APBS in the new pymol 1.5.
We use exactyl this version:
This Executable Build integrates and extends Open-Source PyMOL
†The following error occurs:
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).

ran main.mainCommand
Erasing contents of pymol-generated.pqr in order to clean it up
I WILL RETURN TRUE from pdb2pqr
args=('/software/linuxsoft/pymol/freemol/bin/apbs.exe', 'pymol-generated.in')
Results were:
Return value: 127
/software/linuxsoft/pymol/freemol/bin/apbs.exe: symbol lookup error:
/software/linuxsoft/ifc/compiler60/ia32/lib/libimf.so: undefined symbol:

Could not find pymol-generated.dx so searching for pymol-generated-PE0.dx
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 'pymol-generated-PE0.dx' exist?

It seems to be a very strange error within the intelfortan compiler library.
However we cannot find so far †solution.
So far we did not find a usable new library version to overcome the problem.
Interestingly the APBS version within pymol build 1.2r3pre using APBS
It works. This was a centos45 version of pymol.

Does anyone has encountered a similar error and found a more elegant solution
than just using an old pymol for such calculations?

Thank you very much in advance for your help an suggestions.

Best Regards

Christian Roth
Institut fŁr Bioanalytische Chemie
Biotechnologisch-Biomedizinisches Zentrum
Fakultšt fŁr Chemie und Mineralogie
Universitšt Leipzig
Deutscher Platz 5
04103 Leipzig
Telefon: +49 (0)341 97 31316
Fax: +49 (0)341 97 31319

Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net