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.