Hello all,
I have been trying to dock a library of ligands to a protein while following the Meiler lab tutorials. While I have been able to prepare most of the prerequisite files, I am unsure how I am supposed to obtain 'crystal_complex.pdb'. Trying to download the protein bound with a ligand .pdb file from the protein data bank and using that as my crystal_complex.pdb does not seem to work. While it seems that options.txt and dock.xml have been set up correctly, protein complex.pdb is the only thing preventing me from running the docking itself.
Every time I attempt to run docking, I get the following error:
ERROR: The native pose passed to InterfaceScoreCalculator does not have chain X
ERROR:: Exit from: src/protocols/ligand_docking/InterfaceScoreCalculator.cc line: 234
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing protocol:
File: src/protocols/ligand_docking/InterfaceScoreCalculator.cc:234
[ ERROR ] UtilityExitException
ERROR: The native pose passed to InterfaceScoreCalculator does not have chain X
The tutorial I have been using has a different crystal_complex.pdb that was already prepared for their complex. For obvious reasons, I need to use a complex of my own. Does anyone know how to create this file?