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docking with capping groups

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docking with capping groups


I am trying to dock a peptide into a protein with rosetta. My peptide and protein have capping groups (ACE, NMA), which are recognized by the relax protocol and incorporated into the terminal residues. I then put the relaxed structures together into a complex.pdb file and tried to run the docking protocol:

\$ROSETTA/main/source/bin/docking_protocol.mpi.linuxgccrelease -database \$ROSETTA/main/database -s ./complex.pdb -nstruct 10 -partners A_B -dock_pert 5 10 -spin -randomize1 -randomize2 -ex1 -ex2aro -use_input_sc 

However, this results in an error about the terminal residue THR:AcetylatedNtermProteinFull. Looks like the docking protocol doesn't have centroid definitions for this residue (see extract from log file at end of message). If I do the same process starting with un-capped structures, then the docking protocol runs successfully. I have a similar problem with a glycosilated residue in the protein: I can get the relax protocol to deal with this correctly (using -include_sugars, etc.) but the docking protocol doesn't work with the resulting files.

Any suggestions on how make the docking protocol work with capped and/or glycosilated residues ?


Extract from log file:

protocols.docking.DockingProtocol: (0) ////////////////////////////////////////////////////////////////////////////////
protocols.docking.DockingProtocol: (0) ///                     Rosetta 3 Docking Protocol                           ///
protocols.docking.DockingProtocol: (0) ///                                                                          ///
protocols.docking.DockingProtocol: (0) /// Dockable Jumps: 1                                                        ///
protocols.docking.DockingProtocol: (0) /// Low Resolution Docking Protocol:   on                                    ///
protocols.docking.DockingProtocol: (0) /// High Resolution Docking Protocol:  on                                    ///
protocols.docking.DockingProtocol: (0) /// Low Resolution Filter:   on                                              ///
protocols.docking.DockingProtocol: (0) /// High Resolution Filter:  on                                              ///
protocols.docking.DockingProtocol: (0) ////////////////////////////////////////////////////////////////////////////////
core.chemical.GlobalResidueTypeSet: (0) Finished initializing centroid residue type set.  Created 102 residue types
core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 0.12 seconds.
core.chemical.residue_support: (0) [ WARNING ] Cannot automatically convert THR:AcetylatedNtermProteinFull to centroid, as it is polymeric/has connections.
core.util.switchresiduetypeset: (0) [ ERROR ] [peptide sequence cut]
core.util.switchresiduetypeset: (0) [ ERROR ] can not find a residue type that matches the residue THR:AcetylatedNtermProteinFull at position 1

ERROR: core::util::switch_to_residue_type_set fails

ERROR:: Exit from: src/core/util/ line: 168

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Sun, 2018-11-04 16:17


I was wondering how you solved this problem? I have the same issue

Wed, 2020-01-22 12:41