Dear developpers,
I am using Open Babel 2.3.2 -- Nov 23 2015 -- 18:51:24
I have found a bug in the generations of lammps data files.
I am converting a PDB file to a lmpdat file using the command
babel -i pdb test.pdb -o lmpdat test.lmpdat
Although the generation of the atoms is done correctly, the bonds are not properly generated.
Attached you will find the input and output files.
Regards,
Sebastián
Can you be a bit more specific about "not properly generated?" I don't use LAMMPS much, so I'm not sure what you might want the lammps file to look like. Do you have an example of a LAMMPS file with bonding information?
The structure of the file is correct. The problem is the connectivity of
the atoms. In the lmp file that I previously attached, some H atoms are
bonded with each other, instead of being bonded to C atoms.
The connectivity in the PDB file is correct.
On Fri, Jan 29, 2016 at 7:49 PM, Geoff Hutchison ghutchis@users.sf.net
wrote:
--
Sebastian Echeverri Restrepo
http://tinyurl.com/sebastianecheverrir
Related
Bugs: #972