Docked proteins separated


I am docking a single chain to a homo-trimer (fixed chain), but in my docked complexes the fixed chain and the chain being docked are separated by like 100 A.

I browsed the forum and according to the info there:

  1. I assigned a single chain label to my homo-trimer
  2. The residue numbering of each monomer in trimer is different = no overlap. However, it is not consecutive, eg., first monomer is resid 1234 to 1667, while the second one is 34 to 524, while the third one is resid 800 to 1233. This is the only thing that comes to my mind.

The whole idea is to dock to the second monomer that is the one in the middle.

Yesterday I tried this same docking scenario, however with 3 different chain labels for each monomer and “consider all chains” options when docking. The run was completed, but it also produced a “separated” case.

I am docking using cross-linking restraints and I dock only to residues of a second monomer. In “monomer to monomer” mode it works, so restraints are fine.

Regardless of the case, after finished run server prints out the following info:
" Post-processing: FAILED (or skipped)", which is obviously not the case, as the post processing has been done.

Any input will be appreciated.


Many possible reasons for this behaviour…

Could be your restraints wrongly defined…

If you want better answers, send us privately a link to your run.

Thanks. I have already sent you a link.