GilsonLabUCSD / pAPRika

Advanced toolkit for binding free energy calculations
BSD 3-Clause "New" or "Revised" License
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Add Bind3P as an option in TLeap module #159

Closed jeff231li closed 3 years ago

jeff231li commented 3 years ago

Seems appropriate to add this water model to pAPRika. The module writes a frcmod file with Bind3P parameter, which is loaded in the input file automatically. Example:

system = TLeap()
system.target_waters = 1000
system.set_water_model("tip3p", model_type="bind3p")
system.template_lines = [
    "source leaprc.gaff",
    "MOL = loadmol2 molecule.mol2",
    "model = loadpdb molecule.pdb",
]
system.build()
jeff231li commented 3 years ago

@slochower can you review this PR, I'll cut a new release once this is merged.

slochower commented 3 years ago

Looks good. I'd add a note in the documentation so there's some discoverability for "bind3p".

codecov-io commented 3 years ago

Codecov Report

Merging #159 (4d68f31) into master (2fe1e4e) will increase coverage by 0.18%. The diff coverage is 100.00%.