Hello Charles, thank you for your answer. With a .psf file I was able to get different results for unlinked and linked isopeptide proteins.
The workflow now looks like this: - Save a pdb and fix it with OpenMM's pdbfixer https://github.com/openmm/pdbfixer - Use `pdb2psf` from XPLOR to create a psf file. - Manually (or programatically) add the Isopeptide bond between the correct atoms. - Instead of protocol.loadPDB() use protocol.initStruct(psf_file) ; protocol.initCoords(pdb_file). Thanks again! Kevin ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
