Disuplhide bonds

Disulfide bonds are currently handled automatically using several disulfide scoring components (i.e. dslf_ss_dst) that favor the formation of disulfide bonds and penalize breaking of disulfide bonds. Are your disulfide bonds breaking during the simulation?

I am currently embarking on the same task. I think what batch2k meant was defining specific disulfides in a protein, aka AA 25 to AA 45. I am trying to use pose.conformation().bond_length() as a way to tell if the correct disulfides have been created. If the wrong one(s) were created during a perturbation step, the pose will revert back to its original form. And eventually, the correct disulfides should emerge. We shall see.

I have tried to use the pose.conformation().bond_length to get information about the bond lengths of disulfides, and after testing it on a known structure with a known disulfide I get:

core.kinematics.AtomTree: unable to find DOF_ID for bond_length: atomno= 6 rsd= 5 atomno= 6 rsd= 35
0.0

Anyone know how to ‘fix’ this?
Anyone else trying something similar?

I think next is to calculate the distance b/t the sulfur atoms using atomS1.xyz – atomS2.xyz, and using it as an identifier of the bond.