[chimerax-users] Re: [ISOLDE] Handling Lys-Asp iso-peptide bonds and D-amino acids

Hi Tristan, Just an update. After some poking around, mostly with the .xml file as previously suggested, I struggled to get the residue parameter files to load. The errors indicated a failure to recognise atom types like "h" (for amide hydrogens) and "ct" (for C-alphas), perhaps suggesting that it was still expecting GAFF-type nomenclature. I noted that the two standard AMBER types that it took umbrage with do not exist in the GAFF list. I wonder if an appropriate .frcmod upstream would have changed the outcome somewhat. Will continue poking around a bit on Monday. Cheers, Yang