modeling 4 linkers between 2 domains

[Anonymous]

Hi, I am modeling linkers between domains. There are 2 domains connected by 4 linkers. When I run FloppyTail application, domain docking is performed as if there are 5 domains sequentially connected by 4 linkers. Is there a way to define movemap so that rosetta will consider 2 domains out of 5 as one domain, and the other 3 domains, as another, so that there are 2 domains.

Thanks

Here are my flags

-database /rosetta3.4/rosetta_database/
-in:file:s infile.pdb
-in:file:movemap linksfile
-packing:repack_only
-nstruct 30000
-out:output
-out:file:silent linker_model.out
-out:file:scorefile linker_model.fasc

My linksfile looks like this

RESIDUE 45 54 BBCHI
RESIDUE 174 183 BBCHI
RESIDUE 270 278 BBCHI
RESIDUE 354 397 BBCHI

[Anonymous]

You can’t have four linkers between two domains; two domains can be linked by at most one linker. What I think you mean is that you have two domains, one linker, and a few flexible loops within your domains?

If that is your case, FloppyTail cannot currently handle it. You can model your loops with loop modeling, and your linker with FloppyTail. Although I have no memory of actually writing it, there is a FloppyTail_loop executable sitting around in my personal folder in the unpublished portion of Rosetta. I can share it with you if you want to give it a shot, but I can’t guarantee it works well.

[Author]

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