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I have some questions about using enzyme design application for my system.
1. I have not used RosettaMatch, but I have a rough complex structure of the enzyme with the ligand. Is it fine to use that or I need to use RosettaMatch?
My goal is to insert a linker fragment into a protein which has a chemically bound ligand. To do that, I have relaxed the structure with the chemically bound ligand and am now trying to insert the linker fragment into my protein using Remodel. The ligand is bound to a CYX residue (modified Cystein) in my protein.
Dear Sir and Madam,
I have performed a lot of attempts in order to conduct the coupled_moves docking with ligand without it protonation. I need to specify that this ligand (in his physiologically active form) has only one Hydrogen on his sulfonamide site. Nevertheless, despite the absence of any other Hydrogens both in input .params, MOL2 and PDB file, a lot of sites (sulfonamide Nitrogen with additional undesirable Hydrogen, as well as some Carbons on a benzene ring and tail) get protonated.
By the way, Ligand_Dock application also protonates all possible ligand sites.
I am working on designing some symmetric structures and am currently using REF2015 + hbnet. In addition, I want to add the buried_unsatisfied_penalty. When I add this term to the score function, it works and can score 'non-symmetrized' structures just fine. However, when I try to score a structure that has been 'symmetrized' I get the following error:
[ ERROR ] UtilityExitException