question: where to find the OPLSAA atom types? (moltemplate interoperability)

[jewettaij]

Hello velocirobbie

I'm trying to combine the LAMMPS data files created by your software with other LAMMPS molecule-builder tools. I have one question:

Does this table contain a complete lookup table between the OPLS atom type numbers (from oplsaa.prm), and all the LAMMPS atom types in the DATA files created by your program? (Or are there some scenarios where the data file will contain additional atom types which are not in this table?)

(I realize the atom type numbers for the OPLS force field will vary depending on whether they come from the files on Jorgensen's web site, or your "oplsaa.prm" file. That's okay. I'm grateful you included the "oplsaa.prm" file with your repository. I am trying to make sure my program understands the meaning of the atom type numbers that you are using.)

Once I can confirm that this is correct, I can make a short script which can translate the LAMMPS data files created by your program into MOLTEMPLATE format. I discovered your repository because a MOLTEMPLATE user recently contacted me to ask me how to combine the files from your repository with moltemplate. (Moltemplate gives users a little more flexibility for customizing the system, adding complex molecules, combining weird force fields, and changing the system geometry.) It would be nice to get our software tools working well together.

-Andrew

[jewettaij]

Here is that script.
README_convert_to_moltemplate.sh.gz
(This is a BASH script that uses the ltemplify.py converter tool.)

Please let me know if you think it would be a good idea to add moltemplate export capability to your python program. The script I included above is a BASH script which invokes "ltemplify.py". However there is also python API for ltemplify.py, so the conversion tool can be run directly from within python. If I hear back from you, I will attempt to make these modifications to your code and submit a pull request so that make-graphitics can export to moltemplate format.

[jewettaij]

Incidentally, when using OPLS, you might want to ask your users to also cite the main paper for Jay Ponder's TINKER program, since it appears as though your "oplsaa.prm" file originally came from the TINKER distribution.. (Perhaps I'm being too paranoid. I also use this TINKER "oplsaa.prm" file in my software. That file is a great resource for OPLS users. For what it's worth, when I released my program years ago, I did reach out to Jay, and this is what he asked me to do.)