Rosetta3 – docking_protocol – fold_tree and number of residues problem

[Anonymous]

I have a problem with protein-protein docking (docking_protocol) that I suspect is related to either too many residues or too many chains. I am trying to dock two protein complexes – one with 2 protein chains and one with 3. The total number of residues is 1593. The complexes obviously remain fixed, but when I start the docking run I get the following error.

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protocols.docking.DockingProtocol: Setting docking foldtree

protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 300 -1 EDGE 1 301 1 EDGE 301 468 -1 EDGE 1 469 2 EDGE 469 843 -1 EDGE 1 844 3 EDGE 844 1218 -1 EDGE 1 1219 4 EDGE 1219 1593 -1

protocols.docking.DockingProtocol:

core.kinematics.FoldTree: FoldTree::reorder( 1 ) failed, new/old edge_list_ size mismatch

core.kinematics.FoldTree: 11 1
core.kinematics.FoldTree: FOLD_TREE EDGE 1 300 -1 EDGE 1374 1219 -1 EDGE 1374 1593 -1 EDGE 920 1374 1 EDGE 301 468 -1 EDGE 468 469 2 EDGE 844 920 -1 EDGE 469 843 -1 EDGE 843 844 3 EDGE 920 1218 -1 EDGE 1218 1219 4

core.kinematics.FoldTree: bad fold tree at edge 1374–1219 !

core.kinematics.FoldTree: FOLD_TREE EDGE 1 300 -1 EDGE 1374 1219 -1 EDGE 1374 1593 -1 EDGE 920 1374 1 EDGE 301 468 -1 EDGE 468 469 2 EDGE 844 920 -1 EDGE 469 843 -1 EDGE 843 844 3 EDGE 920 1218 -1 EDGE 1218 1219 4

core.kinematics.FoldTree:

Segmentation fault
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If I reduce things to a system of just 2 chains, I can verify that the binary works properly. In previous releases of RosettaDock I increased the value of MAX_RES to get this to work, but I have grep’ed for everything I can think of and can’t find a variable I can easily change. Any suggestions on what might be wrong and/or what I can change?

Thanks,

Dave

[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

[Anonymous]

Thanks Steven! This solved the problem.

Dave

[Anonymous]

I asked around – you can also try the partners flag: “-partners ABC_DE”, for example. I’m not sure if it’s in the 3.0 release.

[Anonymous]

Multi-chain docking is supported in the 3.0 release, using the -partners flag (as smlewis describes)

[Author]

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