Reply To: Docking a protein into a symmetrical complex

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April 11, 2011 at 5:29 pm #5352
Anonymous

    My understanding of symmetric docking is that it is to be used in situations where the docking “axis” is also the axis of symmetry. When you have a a homodimer (AB) docking to a monomer (C), you should use the -docking:partners option. For this situation, it would be:

    -docking:partners AB_C

    To make life simpler, I would list the chains in the same order as they appear in the input pdb file. Unfortunately, I don’t know too much about using the symmetry mode, so I can’t be much help for symmetric docking.