Reply To: weird prolines with hydroxyls from fixbb.linuxgccrelease

[Anonymous]

Placing hydroxyprolines is weird. I assume from your tone that you are not deliberately doing anything with hydroxyprolines anywhere in your trajectory. I assume these are the standard hydroxyprolines, like in collagen? http://en.wikipedia.org/wiki/Hydroxyproline

I don’t have a copy of the 3.1 database to check but you probably have something screwy in the params files. You may want to delete your copy and refresh it, (or just use the 3.0 database with 3.1; it’s equivalent for fixbb). You can also look through the files (database)/chemical/residue_type_sets/fa_standard/patches.txt and residue_types.txt and see where the hydroxyproline is and just remove it from the allowed set. You can also try deleting any large files of the pattern (database)/Dunbrack*.lib.bin from your database, maybe they got corrupted somehow (or you moved them between systems)