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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