Hi everyone,
I am posting an updated crosslinking script here as the old thread is closed. Three updates are included as documented in the script header:
# JD 03/09/2015 Fix bug where maxbond turned off atom typing for ewald and atom based charges
# JD 03/10/2015 Configured settings to run with or without GUI
# JD 03/13/2015 On-the-fly conversion limit, eliminating problem of open epoxy rings from deleted xlinks

I am posting an updated crosslinking script here as the old thread is closed. Three updates are included as documented in the script header:
# JD 03/09/2015 Fix bug where maxbond turned off atom typing for ewald and atom based charges
# JD 03/10/2015 Configured settings to run with or without GUI
# JD 03/13/2015 On-the-fly conversion limit, eliminating problem of open epoxy rings from deleted xlinks