What is the easiest way to incorporate disulfide bridges in loop modeling protocole? What flags should I add to loopmodeling protocole?
I used the "detect_disulfide_before_relax" - didn't work.
I added constraints file like below:
AtomPair CB 264 CB 257 HARMONIC 3.85 1.0
AtomPair SG 264 SG 257 HARMONIC 3.85 1.0
together with flags:
add -constraints::cst_fa_file input/file.cst and -constraints::cst_fa_weight 1000.0
Despite the fact, that I already have disulfide bridge in the input structure...And I wanted only to refine the loop with disufide.
I am sure there is an easy explanation, I just didn't worked it out myself. Anybody did?