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>
Attachment | Size |
---|---|
3rh8_AB.resfile.txt | 728 bytes |
3rh8_renum.pdb | 186.21 KB |
design.log | 11.8 KB |
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.
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 !!
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?
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.