I am working on a protein structure which contains a modified amino acid (lysine covalently bound to pyridoxal phosphate). I mutated some amino acids in the crystal structure using Pymol. Now, I want to perform energy minimization of the entire structure. But I get an error due to the modified lysine. What shall I do ??
You’ll probably need to make a parameters file for a noncanonical amino acid (modeling the lysine-pyridoxal phosphate as a single novel amino acid). From this question (https://www.rosettacommons.org/content/creating-new-residue-type-pyridoxal-phosphate-bound-lysine-llp-solved ) it looks like the HowToMakeResidueTypeParamFiles documentation in the demos directory (under demos/protocol_capture/2010/using_ncaas_protein_peptide_interface_design ) was sufficient for another user to get it to work.
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