AMBER protein atom types are upper case, whereas GAFF types are lower case. So the AMBER atom type for C-alphas (sp3 aliphatic C) is “CT” and for amide hydrogens (H bonded to nitrogen atoms) is “H”. Such as: ambermini-share-amber-dat-leap-parm-parm99.dat at master · choderalab-ambermini

—Eric

On Apr 19, 2025, at 3:44 PM, Yang Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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
_______________________________________________
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/