Validate parameters - Githubissues

rsdefever / GAFF-foyer

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Validate parameters #2

Open ahy3nz opened 5 years ago

ahy3nz commented 5 years ago

Use antechamber + tleap to get some amber files
Use mbuild + foyer + gaff-foyer to get some amber files
Eyeball and compare the values
Make two parmed structures and commpare energies
I think the bonds/angle force constants were correct, but periodic torsions might be off by factor of 2?

rsdefever commented 5 years ago

As far as an eyeball check is concerned, see: https://github.com/choderalab/openmm-forcefields/blob/master/amber/ffxml/gaff.xml

For periodic torsions, see documentation here. I think I am handling those correct. http://ambermd.org/FileFormats.php#parm.dat

Still agree that commpare and antechamber+leap vs. foyer will be good comparisons.

Leaving issue open for now.

ahy3nz commented 5 years ago

I haven't gotten to torsions or nonbondeds, but the bond and angles look to be in agreement. You can make a foyer forcefield or an openmm force field, and call forcefield.getGenerators() to start looking at the various parameters in each FFXML. It's a little harder to compare the artificial atomtypes if they don't have the corresponding atomtypes