Incorrect atom types in PSF when using gaff.xml

[jpotoff]

@rsdefever

I'm continuing my quest to develop some robust workflows for GOMC and found some strange behavior when loading gaff.xml and using it to assign parameters. The parameter file that is produced looks fine, but in the PSF file, the atom types (column 6 in the PSF), and partial charges are set incorrectly.

I'm a bit mystified as to where C3LTU and HCLTU (atom types) are coming from, since they are nowhere to be found in gaff.xml. Thoughts?

test.zip

[rsdefever]

Partial charges in GAFF come from RESP --> so all the partial charges in gaff.xml are set to 0.0. antefoyer can call antechamber to extract AM1-BCC charges. Writing a QM+RESP module for MoSDeF is on my radar. If this is something you are also interested in we should chat.

The C3LTU atom types are a bit more mysterious. They seem to be added by the .save function (this is a parmed function.

Here is a minimal example:

import mbuild
import foyer

ff=foyer.Forcefield(forcefield_files='gaff.xml')
ethanol = mbuild.load("CCO", smiles=True)
ethanol_param=ff.apply(ethanol, assert_dihedral_params=False, verbose=False)

print(ethanol_param[0].type)

ethanol_param.save('ethanol.psf', overwrite=True)

print(ethanol_param[0].type)

[ahy3nz]

Quick glance at parmed, here and here

[jpotoff]

Quick glance at parmed, here and here

def _typeconv(name):
    if isinstance(name, integer_types):
        return name
    if name.upper() == name:
        return name.replace('*', 'STR').replace('+', 'P').replace('-', 'M')[:6]
    # Lowercase letters present -- decorate the type name with LTU --
    # Lower To Upper
    return ('%sLTU' % name.upper()).replace('*', 'STR').replace(
            '+', 'P').replace('-', 'M')[:6]

Ok, I have to say that's a bit weird. This has got to be a bug appending "LTU" to lower case atom types. Why would anyone want that behavior?