I'm trying to use the membrane ab initio modeling application (membrane_abinitio2). I have followed the instructions in the "membrane_abinitio" demo directory and it did work.
My question is: can I add constraints (such as disulphide bonds) and NMR restraints (such as RDC measurements) in the process?
I tried to add -fix_disulf and -score:patch flags in the command but it didn't seem to affect the outputs. The score file did not have "rdc" terms in it and the structures did not satisfy the disulphide bonds.