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
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2012/9/27 Christian Roth <christian.r...@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 für Bioanalytische Chemie
> Biotechnologisch-Biomedizinisches Zentrum
> Fakultät für Chemie und Mineralogie
> Universität Leipzig
> Deutscher Platz 5
> 04103 Leipzig
> Telefon: +49 (0)341 97 31316
> Fax: +49 (0)341 97 31319
>
>
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