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What's a good source for geometric parameters?

  1. We could borrow geometry from particular open force field implementations (OpenMM; AMBER-FB15 are the first two I thought of/glanced at). Advantage: quicker compatibility with those force fields, existing code to map structure files to usable objects. Disadvantage: perception, real or purely... perceptual, of being locked to/preferring that style of modeling.
  2. We could read in the Chemical Component Dictionary and transform each set of monomer parameters into a usable representation. Advantage: massive coverage (including immediate extension to NCAAs/ligands when we're brave enough); disadvantage: there are sometimes surprising errors, so outside of the canonicals (where of COURSE we're hand-curating), we will need to be judicious; no preexisting code for processing.

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