Open JoshuaSBrown opened 5 years ago
It's been a while but at a quick glance, I do not think we ever got around to implementing this in the LAMMPS parser: https://github.com/shirtsgroup/InterMol/blob/master/intermol/lammps/lammps_parser.py#L401
https://github.com/shirtsgroup/InterMol/blob/master/intermol/lammps/lammps_parser.py#L394
Just a heads up, I have just been made aware that there is this package that provides file parsing capabilities for several molecular dynamics file types. You might already be aware.
https://www.mdanalysis.org/docs/documentation_pages/topology/init.html
And I'll see if I can fix the issue.
Last I checked MDAnalysis did not read or convert forcefield parameters but it's been a while since I tried it.
The other package that we've been involved in is https://github.com/ParmEd/ParmEd which does perform full forcefield parameter conversions but does not yet support LAMMPS. ParmEd is actually how InterMol operates on Amber files: https://github.com/shirtsgroup/InterMol/blob/master/intermol/convert.py#L641
E.g. Here is a section from a lammps.data file that is in the
Atoms
section notice that the molecular tag changes at atoms 517 to 518.And here is the output from the converted gromacs file created using intermol:
Notice that the residue number has not been changed to indicate that the atoms are on a separate molecule. They are all considered to be on residue 1.