How can we specify additional forcefield loading statements for LEaP?

For dealing with divalent cations, we need to do more than load a leaprc.* file.

There is an additional step of loading another frcmod file:

source leaprc.ff14SB 
loadAmberParams frcmod.ionslrcm_hfe_tip3p 

Do we currently have the capability to specify these extra lines to be passed to leap?

[andrrizzi]

Currently parameters handle both .frcmod and .leaprc files. This can work because it loads by default the leaprc.gaff with small molecules.

If we plan to move away from leap, maybe it’s better to expand the syntax to load multiple parameters files (and use the right command based on the extension)? Something like

molecules:
  peptide:
    filepath: peptide.pdb
    parameters: {leaprc.ff99SB, frcmod_S2P, S2P.off}
    strip_protons: yes

[jchodera]

Note that the OpenMM setup pipeline won’t be in YANK 1.0