You are here

Errors in Interface design  

5 posts / 0 new
Last post
Errors in Interface design  

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 ( 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
-nstruct 2                    # Generate 2 models
-s 3rh8_renum.pdb                # Use structure 3rh8 as input

Xml file  design.xml

        Include rotamer options from the command line
        <InitializeFromCommandline name="ifcl" />
        Design and repack residues based on resfile
        <ReadResfile name="rrf" filename="3rh8_AB.resfile"/>
        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" />
        Run the design protocol
        <Add mover="design" />

        Calculate interface metrics for the final sequence
        <Add mover="analyze" />
    <OUTPUT scorefxn="REF2015" />

3rh8_AB.resfile.txt728 bytes
3rh8_renum.pdb186.21 KB
design.log11.8 KB
Post Situation: 
Thu, 2019-10-31 17:48

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.

Thu, 2020-01-30 15:40

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 !! 

Mon, 2020-05-18 10:49

Just curious, which tutorial in the Meiler lab link you provided ( did you get the .xml file from?

Fri, 2020-02-28 19:37

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. 

Mon, 2020-05-18 10:52