Den 2019-10-18 kl. 23:04, skrev Geoffrey Hutchison:
How about Gaussian log files? It works with those as well.
Somehow there bond orders are derived correctly as well although no such
information is extracted from the log files.
Are you saying that PDB is giving you different information than the Gaussian
files? If so, I'd be curious to see some files.
-Geoff
I've uploaded a file to my work webserver
http://folding.bmc.uu.se/diethyl-sulfate-3-oep.log.gz
Using the master branch, freshly updated and built:
% obenergy -ff GAFF diethyl-sulfate-3-oep.log.gz
<snip>
3 os NO
4 s6 NO
5 os NO
6 o NO
7 o NO
<snip>
Now, using pdb:
% obabel -ig09 diethyl-sulfate-3-oep.log.gz -opdb -O test.pdb
1 molecule converted
% obenergy -ff GAFF test.pdb
<snip>
3 os NO
4 s6 NO
5 os NO
6 oh NO
7 oh NO
<snip>
(note that no hydrogens are added but the atomtype changes).
Possibly related to this is that conversion to sdf seems to have changed
for this compound from version 2.4.1 to master (3.0). The double bonds
S=O have disappered, however there is another change in the sixth column
after the element symbol:
% diff ds2.4.1.sdf ds3.0dev.sdf
10,11c10,11
< 0.0001 1.2905 -1.2428 O 0 0 0 0 0 0 0 0 0 0 0 0
< -0.0002 1.2905 1.2428 O 0 0 0 0 0 0 0 0 0 0 0 0
---
> 0.0001 1.2905 -1.2428 O 0 0 0 0 0 1 0 0 0 0 0 0
> -0.0002 1.2905 1.2428 O 0 0 0 0 0 1 0 0 0 0 0 0
29c29
< 4 7 2 0 0 0 0
---
> 4 7 1 0 0 0 0
32c32
< 6 4 2 0 0 0 0
---
> 6 4 1 0 0 0 0
To make things more complicated the charges generated are different for
the two SDF file as well...
Sorry for the long message!
--
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
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
