On Fri, Feb 1, 2013 at 5:40 PM, Xing <xi...@pitt.edu> wrote:
>
> Dear all,
>
> The attached pdbs are two identical files from Protein Data Bank. The one
with the original name "2K4G.pdb" will cause Avogadro 1.1.0 to crash (see
2K4G.log) and just changing the name from "2K4G.pdb" to "2K4G_avo.pdb" will
prevent the software from crashing. Avogadro 1.0.3 does not have this
problem. Maybe it's related to the new Open Babel version (2.3.1) ?
Actually this happens to various files containing large molecules and the
error messages are usually different from one to another.
>
> I can reproduce the bug on both Windows 7 and OpenSUSE 12.2 platforms. Am
I the only one facing the problem or maybe it is really a bug?
Definitely an odd bug, one that I cannot reproduce here.
But, digging through the sources, I find the error message at the end of
the .log file in the openqube mopac .aux file reader. Are there any files
in the directory with 2K4G.pdb that have a .aux (or similar) extension? Or
have you done any MOPAC calculations on it?
Does it work if you move the pdb file to another directory?
I don't see this particular error message anywhere else in openbabel or
avogadro, so it definitely seems to be because of a bad .aux file.
If you still see this issue with the pdb file in another directory, we'll
need to get a backtrace of the crash to really track this down.
> Department of Chemistry
> University of Pittsburgh
Perhaps Dr. Hutchison could help with the debug build/backtrace if needed
;-)
Dave
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