Errors in Interface design  

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    • #3288
      Anonymous

        Hello there, Now I’m trying to optimize the protein sequence at binding interface for increased affinity to its target. A complex structure was previously solved by X-ray crystallography (PDB 3rh8). To make their affinity higher, I would like to design the protein sequence at both sides. Meiler Lab provides a step-by-step tutorial at his website (http://www.meilerlab.org/index.php/rosetta-tutorials). According to his tutorial, I tried, but I found something like error.

        I could not get any model. I appreciate if you could tell me how to solve this error. I attached all input files (pdb, resfile, options, xml files) and generated error (log file).  

        Command line I typed

        ~/rosetta_src_2018.33.60351_bundle/main/source/bin/rosetta_scripts.macosclangrelease @design.options -parser:protocol design.xml -out:suffix _design -scorefile design.fasc > design.log

        flags I used   design.options

        -linmem_ig 10                        # limit memory to store rotamer pair interactions

        -use_input_sc                        # Include rotamers from the input structure

        -ex1

        -nstruct 2                    # Generate 2 models

        -s 3rh8_renum.pdb                # Use structure 3rh8 as input

        Xml file  design.xml

        <ROSETTASCRIPTS>

            <SCOREFXNS>

            </SCOREFXNS>

            <TASKOPERATIONS>

                Include rotamer options from the command line

                <InitializeFromCommandline name=”ifcl” />

                Design and repack residues based on resfile

                <ReadResfile name=”rrf” filename=”3rh8_AB.resfile”/>

            </TASKOPERATIONS>

            <MOVERS>

                Design the antibody interface

                <PackRotamersMover name=”design” scorefxn=”REF2015″ task_operations=”ifcl,rrf” />

                Analyze the resulting interface

                <InterfaceAnalyzerMover name=”analyze” scorefxn=”REF2015″ packstat=”0″ pack_input=”0″ pack_separated=”1″ fixedchains=”A” />

            </MOVERS>

            <FILTERS>

            </FILTERS>

            <APPLY_TO_POSE>

            </APPLY_TO_POSE>

            <PROTOCOLS>

                Run the design protocol

                <Add mover=”design” />

                Calculate interface metrics for the final sequence

                <Add mover=”analyze” />

            </PROTOCOLS>

            <OUTPUT scorefxn=”REF2015″ />

        </ROSETTASCRIPTS>

      • #15130
        Anonymous

          This is related to a bug in the Rosetta 3.10 release. Using a more recent release (like Rosetta 3.11 or a weekly on or after the 2018.42 one) should avoid this issue.

          • #15292
            Anonymous

              My apologies for late reply to you. 

              Thanks to your advise, I successdully solved this problem by using the recent version of Rosetta3.12. 

              Thank you very much !! 

          • #15174
            Anonymous

              Just curious, which tutorial in the Meiler lab link you provided (http://www.meilerlab.org/index.php/rosetta-tutorials) did you get the .xml file from?

              • #15293
                Anonymous

                  I’m sorry for late reply. I got this xml file from Rosetta Antibody Workshop 2019. 

                  By updating the Rosetta version, everything is going well right now. 

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