List of known unknown concerns

nhenriksen / speakeasy

Automates the conversion of SMIRNOFF parameters to AMBER force field files

MIT License

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Open nhenriksen opened 6 years ago

nhenriksen commented 6 years ago

Where does AMBER do logic that is hard coded for specific atom types?
Does tleap add improper torsions based on some internal chemical perception which is hardcoded to atom types?
We will probably want to enable "lower case only" mode, so there is no conflict with other Amber ff's

slochower commented 6 years ago

How can we effectively parse the bonds in the OpenMM System? I know how to do this for ParmEd, but I don't know how to effectively do this in OpenMM. The documentation suggests it won't be too difficult.