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docking with constraints

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docking with constraints

Hi there,

I am trying to performe a docking simmulation between two proteins, A and B. I know that two atoms, one from each protein, are about 3 A away. I am trying to run a docking simmulation with this constrain but knone of the output models fulfill this restrain. Could you please help me with this? Yo can find below configuration and constrains file. I have already tryed with many diffrent constrain functions
Thanks in advanced.



-database /home/Local_Programs/rosetta_database/
-in:file:s dotu.pdb
-dock_pert 1 1
-out:nstruct 200
-out:file:o score
-out:prefix dotu_modecoy
-constraints:cst_file constraint.cst
-out:path:pdb /home/Work/docking/rosetta


AtomPair OG1 382 NE2 459 SCALARWEIGHTEDFUNC 100000 HARMONIC 2.6 0.2

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Tue, 2013-05-07 01:50

I'm surprised you're not getting an error message.

One key point is that Rosetta has two major modes - fullatom and centroid. Full atom is with all the atoms, whereas centroid mode uses a reduced sidechain representation and a united-atom backbone model. Most protocols use fullatom, but things doing major rearrangements, like loop modeling and docking, often have stages where they run in the simpler centroid mode to speed things up.

The -constraints:cst_file sets the *centroid* mode constraints. Not only is the given file only active in centroid mode, because it's centroid, it doesn't have any sidechain atoms like OG1 and NE2 to constrain. What you want is to use the fullatom constraint file flag, -constraints:cst_fa_file. Keep in mind, though, that that file will only be active during the fullatom refinement stage. It won't apply during the coarse centroid sampling. I would recommend making another constraint file for centroid mode, based off of the CA distances, and pass that to the -constraints:cst_file option along with the sidechain atom constraint file passed to the -constraints:cst_fa_file option.

Tue, 2013-05-07 11:56