Like some others on this forum, I'm having some trouble getting disulfides to work. I pass
where disulf is a text file containing the residue numbers of the cysteines I am trying to bridge like so:
With an empty line at the end, which others have mentioned may be necessary. Unfortunately, this has no discernable effect on the loop in question--I have done pretty extensive testing, and I never see a disulfide form. Should I try to encode this disulfide as a constraint, or is there something I'm clearly doing wrong?
Given that -in:fix_disulf has no effect by my lights, can any of you suggest a benchmark or standard to test whether this command is working properly in my installation? I've had success with other projects, so it would have to be a pretty specific issue.
-in:fix_disulf (note the underscore and not a colon between fix and disulf) is handled at the application level, rather than at a general Rosetta level - depending on your protocol it may not even be read. Which protocol are you using?
If your protocol does not obey -in:fix_disulf, then (atom pair) constraints may be the way to go - many protocols, even if they don't obey -in:fix_disulf, will automatically detect disulfides if the two cysteines are close enough.
For an example of -in:fix_disulf usage, you can take a look at Rosetta/demos/protocol_capture/2012/replica_docking/, which makes use of it.
Looking back at what I've done, I was passing -in:fix_disulf with correct punctuation, I just reproduced it incorrectly in my first post.
I'm using a homology modelling protocol to do loop building on a membrane protein, here's the contents of the options file:
-loops:loop_file ./test.loops ##loop file
-ex1 #Include extra chi1 rotamers
-loops:frag_sizes 9 3 1
-loops:frag_files ./aat000_09_05.200_v1_3 ./aat000_03_05.200_v1_3 none
Any idea what the problem might be? I've begun to try using an atom pair constraint, we'll see how that goes.
EDIT: For anyone with similar problems, I seem to have successfully generated disulfides by passing this constraint file:
AtomPair SG 269 SG 280 HARMONIC 1.800 2.05
with these options: