Reply To: Rosetta3 – docking_protocol – fold_tree and number of residues problem

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September 7, 2009 at 2:56 pm #4179
Anonymous

    Dave,

    We have a separate forum now for rosetta_3 stuff – look at the forums link at the top of this page. Just FYL.

    The problem is too many chains – the legacy problem of too many residues has gone away forever. (Well, it’s now limited by the memory on your computer, not some arbitrary array, anyway).

    The easiest quick fix is to just hack your PDB file to make it look like the two complexes are just two chains – this should work fine so long as there are no termini at the interface (this will cause defective termini detection).

    You can do that by removing any “TER” lines in the PDB and making the first complex all chain A and the second all chain B.

    There may be an easy flag to fix this I’m not aware of; I’ll ask around.

    Steven