Hi Yang,
I'm not certain what parameters exactly you need, but you can get ChimeraX to give you partial charges and GAFF atom types for the isopeptide-bonded residues.  First you would give the residues non-standard names so that ChimeraX doesn't just look up the parameters in a table, e.g.:

setattr residue1 r name XXY
setattr residue2 r name XXZ

The you just run Add Charge on your structure.  You can write out the GAFF types and partial charges using Mol2 format, e.g.:

save ~/parameterized.mol2 gaff true

--Eric

On Apr 9, 2025, at 7:19 AM, Yang Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Tristan and Eric,

From hopelessness, I find myself newly heartened!

I tried but failed to find mention of this isopeptide bond treatment in the original Chimera mailing list archives. Is the procedure mentioned here already part of the Add Charge menu function or a lower level function I can adapt? Also, is it something that can be easily jerry-rigged into ISOLDE's minimisation perhaps with a code change?

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/