I'm quite new to all of this, so please let me know if I've missed anything. I've been tasked with designing a more thermodynamically stable protein to catalyze a reaction. I made a resfile for the new amino acid, made a constraints file, and pointed to the constraints in the PDB header. It seems to run (It discards some atoms and tells me there's no appropriate entry found in a constraint). Despite running successfully, it doesn't seem to actually change the structure. The most it's done is removed the leading residue in the PDB and spat it back out. Have I overconstrained it or is one of the warnings causing this issue?
Thank you so much for your help!
Header (PDB was too big):
REMARK 666 MATCH TEMPLATE H SeN 22 MATCH MOTIF P CYS 410 1 1
REMARK 666 MATCH TEMPLATE H SeN 22 MATCH MOTIF P TYR 351 2 1
REMARK 666 MATCH TEMPLATE H SeN 22 MATCH MOTIF P THR 412 3 1