Now, I am trying to docking protein A to selected surface region of protein B in my . In the calculation, I set solvent accessible surface residues (surface area > 50 Ang.^2) of protein A to be active sites.
For protein B, I had tried two ways. One way is seting SASA on the selected region of protein B as the active site. And randomly AIRs definition is turned off (ranair=false in run.cns). But this jobs fails, beacuase of too many structures fail in it0 stage. (In another protein docking test with different molecules, this is ok.) Although I have searched the solution in forum in which suggestion is to change the random seed. I have try this, but it doesn’t work. The following is the error information for other to locate this issue:
HADDOCK cannot continue due to failed structures in it0
HADDOCK could not copy failed structures from previous iteration
The following structures could not be docked:
The another way is that leaving protein B’s active residue setting blank and set the nseg_B = 1, and B_start_seg_1=“1”; B_end_seg_1=“410”; ranairs=false. However, there are also many structures failed in it0 stage and I kill the job. By the way, after killing the job by job system command, the KeepAlive.py will keep generate the out file. So I have to the node to kill the KeepAlive.py job. Counld I have more convinent way to clean the jobs by haddock-clean.py script??
So, are so many failed structures caused by the incorrected setting of active residues? In semi-flexible segment setting, many residues in squence B_start_seg_1 to B_end_seg_1 are not surface residues. Does it cause problems? If it is, how to set the discreted surface residues ID in this part.
Thanks Very Much for your time and Response!!!