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#972 Bug generation of bonds lmpdat

2.3.x
open
nobody
Lammps (1)
1
2016-01-29
2016-01-21
Sebastian ECHEVERRI RESTREPO
No

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

2 Attachments
test.lmpdat
test.pdb

Related

Bugs: #972

Discussion

  • Geoff Hutchison

    Geoff Hutchison - 2016-01-29

    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?

     

    • Sebastian ECHEVERRI RESTREPO

      Sebastian ECHEVERRI RESTREPO - 2016-01-31

      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:

      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?

      Status: open
      Group: 2.3.x
      Labels: Lammps
      Created: Thu Jan 21, 2016 10:57 AM UTC by Sebastian ECHEVERRI RESTREPO
      Last Updated: Thu Jan 21, 2016 10:57 AM UTC
      Owner: nobody
      Attachments:

      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

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      --
      Sebastian Echeverri Restrepo
      http://tinyurl.com/sebastianecheverrir

       

      Related

      Bugs: #972