Member Site › Forums › Rosetta 3 › Rosetta 3 – General › Errors in Interface design
- This topic has 4 replies, 3 voices, and was last updated 4 years, 6 months ago by Anonymous.
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November 1, 2019 at 12:48 am #3288Anonymous
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>
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January 30, 2020 at 11:40 pm #15130Anonymous
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.
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May 18, 2020 at 5:49 pm #15292Anonymous
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 !!
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February 29, 2020 at 3:37 am #15174Anonymous
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?
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May 18, 2020 at 5:52 pm #15293Anonymous
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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