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Full Protocol

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Full Protocol


I am a newbie to RosettaDock, so this query might be a trivial one for some. I am trying to perform protein-protein docking with the "Full Protocol". What I understood from the manual, for using this protocol, no additional flag is required. I did the same but all I got was an error. This is what I used:
/path/rosetta_source/bin/docking_protocol.linuxgccrelease \
-database path/rosetta_database\
-s combined.pdb \
-nstruct 3000\
-ex1 -ex2aro \
-use_input_sc \
-partners Y_X \
-dock_pert 3 8 \
-mute \
-out:overwrite -out:file:fullatom \

So as the manual says, "Default mode of docking. No additional flags necessary.", I did not define a flag for docking. And the error I am getting is the following:
"can not find a residue type that matches the residue PRO_p:pro_hydroxylated_case1at position 35

ERROR: core::util::switch_to_residue_type_set fails

ERROR:: Exit from: src/core/util/ line: 135"

Please help.

P.S. Which protocol should be used to get better docking results: Full protocol or High Res docking?

Post Situation: 
Fri, 2013-10-04 01:07

You have an issue with your input PDBs, particularly with the hydrogens. There are several alternative naming conventions with hydrogens, and in some instances Rosetta will get confused by them, and think a normal proline is a hydroxylated proline, because of the hydrogen naming. This should be fixed in the more recent weekly releases, but the simple fix is just to delete all the hydrogens (or just the proline hydrogens) from the input PDB. (If you've already passed the structure through Rosetta once, you may need to also delete the spurious hydroxyl oxygen atom that's been added to the proline). This is easy enough to do with a plain text editor (especially ones like emacs or vim), or can be automated with tools like awk, sed and grep. Rosetta will be able to add back the missing atoms with no difficulties.

"Better" docking results are somewhat dependant on your case. If you already have the complex in the known generally correct binding orientations, then you can skip directly to High Res docking. If you need to find the binding interface/orientation, then you should use the Full protocol to do the low resolution search step to find that interface/orientation.

Tue, 2013-10-08 08:21