Den 2018-03-07 kl. 08:17, skrev David van der Spoel:
Den 2018-03-07 kl. 04:15, skrev spamidig:
Geoffrey, David:
Here is what I have for the openbabel on the g09 output file. Please
let me
know if you can not get the file as uploaded.
Thanks,
Sudhakar.
../openbabel-2.3.2/build/bin/obabel -i g09 gaussian.log -o copy -O
obab.copy
--errorlevel=2
0 molecules converted
root@2d3f3e9bd2f0:/datacat/working-dir#
../openbabel-2.3.1/build/bin/obabel
-i g09 gaussian.log -o copy -O obab.copy --errorlevel=2
0 molecules converted
gaussian.log <http://forums.openbabel.org/file/t375565/gaussian.log>
I can reproduce the issue als with version 2.4.1 of OB.
Apparently no atoms can be read as it leaves the routine for readin
gaussian files at this point:
// done with reading atoms
natoms = mol.NumAtoms();
if(natoms==0)
return false;
The problem appears because the code is looking for a keyword
"orientation" which can be used as in "Standard orientation:" or, in
your file, "Dipole orientation:". obabel picks up the second one and
assumes the coordinates come after that, but they don't.
Is there any reason not to change gaussformat.cpp around line 513
}
if (strstr(buffer,"orientation:") !=NULL)
{
to
}
if (strstr(buffer,"Standard orientation:") !=NULL)
{
--
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David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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