Errors in Interface design

[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>

[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.

[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 !! 

[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?

[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. 

[Author]

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