(The section below overlapped with this and resolved the issue)
CD – “Bond between monomers” bug - No chemical info is assigned to bond between monomers. Should this get the same treatment as the PEPTIDE_BOND in proteins, or should I do something more general?
Issue is that the bond assignemnt…
The peptide bond assignment code/SMARTS can’t include hydrogens because they are immediately made nonnegative upon matching the first time. This could be resolved by NOT making the Hs negative immediately upon matching a template.
Should we make “overwriting bonds” only apply to bonds between tagged atoms?
Should there be special SMARTS that only apply to atoms that are unspecified at the time that the matching is run?
CD – Should it be allowed to assign different chemical structures for things like electronegative neighboring monomers?
JW – I think things like that are best handled by the FF itself, we don’t want to creatively interpret kekule structures to assign the parameters we want, we should instead just add parameters to the FF to assign the parameters we want.
CD – Getting a way to get unique atom identifiers in PDB (when the original file doesn’t have unique atom identifiers). That is, OpenMM won’t accept the same atom name multiple times.
CD – I have a hacky workaround here where I add characters after the element symbol
JW – That’s probably about as good as you can do, unfortunately. This wouldn’t be an issue if the original file had different residue names/numbers but the file you’re showing is just 6000 atoms in one residue.