I've been trying to readapt the ligand_docking tutorial (provided by the Meiler lab's Rosetta Virtual Workshop 2020 youtube series) to dock a Heme porphyrin to protein 4K8F. In short, I am having issues with the dock.xml file, specifically with the <InterfaceScoreCalculator> mover and its -native flag for generating alignment results to a given protein-ligand complex. When including <InterfaceScoreCalculator native="crystal_complex.pdb">, my ligand_docking run produces a ROSETTA_CRASH.log error, "Residue out of res_map range"". I believe the issue is my "crystal_complex.pdb" file for 4K8F bound to heme.
I'm curious if anyone knows whether the "crystal_complex.pdb" file needs to be prepped in a particular manner in order to be used with <InterfaceScoreCalculator> and its -native flag???
The attached ligand_docking tutorial states that the provided crystal_complex.pdb file "was taken directly from the RCSB PDB [for D3R and its bound ligand eticlopride]", but says little else... So, to produe an analagous file for 4K8F and HEME, I performed the following steps:
(1) From the RCSB PDB I downloaded biological-assembly-1 for 4K8F. This file contained a homodimer made from two 4K8F-heme complexes.
(2) I deleted chain-b and the second heme-ligand information from the pdb file, so that only one monomer-ligand complex remained within the pdb file.
(3) I changed all HETATM records to indicate chain X instead of A for HEME ligand.
(4) I renamed this file "crystal_complex_4K8F.pdb"
Finally, after making crystal_complex_4K8F.pdb, I ran the ligand_docking application using ROSETTA binaries via comamnd line:
~/rosetta/main/source/bin/rosetta_scripts @options.txt -nstruct 500 > ligand_docking.log
This is where I am currenly stuck ... Any tips or suggestions would be greatly appreciated. Please let me know if I need to reclarify.
P.S. I can confirm that when calling my dock.xml and options.txt files, without the -native flag in mover <InterfaceScoreCalculator>, the ligand_docking application works correctly and produced good results - i.e. all of my docking outputs were RMSD 0.00 when aligned to the native crystal structure in PyMOL (as expected). Unfortunately, the heme ligand was not included in these PyMOL structural alignments, hence why I am now trying to run ligand_docking again with <InterfaceScoreCalculator native="crystal_complex.pdb">.