Hi Christian.

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

reinitialize
fetch 4ins, async=0

import os
print os.environ['temp']
print os.getcwd()
os.environ['temp']=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 :-)

Best
Troels Emtekśr Linnet
Ved klÝvermarken 9, 1.th
2300 KÝbenhavn S
Mobil:
+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 1.5.0.4.
†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
GENERATED
Running:
prog=/software/linuxsoft/pymol/freemol/bin/apbs.exe
args=('/software/linuxsoft/pymol/freemol/bin/apbs.exe', 'pymol-generated.in')
Results were:
Return value: 127
Output:
/software/linuxsoft/pymol/freemol/bin/apbs.exe: symbol lookup error:
/software/linuxsoft/ifc/compiler60/ia32/lib/libimf.so: undefined symbol:
__aullshr

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
--
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

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