Hello Kevin-- > > 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.
There is an example of using a script for this in eginput/PSF_generation/isopeptide.py in the Xplor-NIH distribution. > - Instead of protocol.loadPDB() use protocol.initStruct(psf_file) ; > protocol.initCoords(pdb_file). > Sounds like you got it! Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
