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:
-s combined.pdb \
-ex1 -ex2aro \
-partners Y_X \
-dock_pert 3 8 \
-mute core.util.prof \
-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/SwitchResidueTypeSet.cc line: 135"
P.S. Which protocol should be used to get better docking results: Full protocol or High Res docking?