requesting meaningful OPLSAA atom types in output files

[jewettaij]

• [ ] I believe this to be a bug with LigParGen
• [x] This is a feature request

Issue Information

Software name & Version : http://zarbi.chem.yale.edu/ligpargen/ Method: Not relevant (1.14*CM1A for charges, if it matters)

Expected Behavior

We would like LibParGen to report the atom type strings that it uses for force-field lookup in the files that it creates. I am specifically asking for the atom type names that are used for looking up force-field parameters in the official OPLSAA files (distributed here and here). These atoms have names like "C135", "C137", "C283", "H140" (not "CA" or "C01". Those are PDB atom-names. That's not what we need.)

I explain why this would be very useful below.

It would be great if all of the files generated by LibParGen included these atom type names, but we would be happy to settle for Charmm RTF and PRM files for now. (OpenMM/FF XML and LAMMPS would be great too.)

I'd also request the the output files include a time and date. The reason I ask this is because it is important to know which version of the OPLSAA force field was used, and this can (hopefully) be inferred from the date. (I suspect that these atom type strings might vary depending on the version of OPLSAA you are using. If so, perhaps you could include the date somewhere in the headers of the files you create? Or in the file names?)

Actual Behavior

Currently each atom is assigned to a unique (automatically generated) type name even if there are multiple copies of the same atom in the molecule.

Also, if you run LibParGen twice on two different molecules, there is a high chance that they will both contain an atom of type "C801" (for example), even though (I suspect) that atom type probably refers to something different in those two molecules. This makes it hard to combine two different molecules in the same simulation.

Benefits of revealing atom types

1. Allow users to combine multiple different molecules together in the same simulation without having to worry about atom type name collisions.
2. Reduce the number of questions you receive from users wondering why LibParGen generated a molecule with unexpected force field parameters. (I see many issues like this on the issue-tracker.) LibParGen is currently a black box. Let users look inside the box (a little bit) and answer their own questions.
3. Make it easier for third-party developers (such as myself) to write tools which can convert LibParGen output files into new formats.

I'm currently trying to release a tool which will convert LibParGen into moltemplate format. This will make it significantly easier for LAMMPS users to benefit from LibParGen. (Moltemplate is a molecule-builder for LAMMPS. I wrote moltemplate.) Hiding the atom type makes this task much harder.

Is there a reason atom types are hidden? Are there some atom types generated by LibParGen that do not correspond to anything that's in the OPLSAA force field files? (If that is the case, would you be willing to consider reporting the atom type names for the subset of atoms which are defined in the official OPLSAA files?)

Thanks in advance for your time and consideration.