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Error when trying docking protocol with different ligand

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Error when trying docking protocol with different ligand


I'm coaching an iGEM team at the University of Warwick and they're doing some dock design to try to switch the specificity of a transcription factor to a different ligand. We've been able to run the docking protocol with the protein and it's native ligand and it is able to recapitualte the the native binding. However, when we try the docking protocol with the new ligand we run into this error:

File: src/core/io/pose_from_sfr/
[ ERROR ] UtilityExitException
ERROR: The last residue, residue188 named "ACE" has been indicated to merge with the next residue from the core::io::NomenclatureManager

 Looking at the PDB files and the params files there are no obvious differences between the two aside from the different ligand and it's coordinates. I was wondering if you could offer any advice.



Post Situation: 
Wed, 2020-08-05 04:37

I had an issue with ACE as a name in pyrosetta. This is normally an acetyl group or acetate. And even if you have `-load_PDB_components false` it will refuse the params file. It is a standard residue type. In pyrosetta this gives me an acetyl group (*C(=O)C)

pose = pyrosetta.Pose()
rts = pose.conformation().modifiable_residue_type_set_for_conf(pyrosetta.rosetta.core.chemical.FULL_ATOM_t)
# add new residue
lig = pyrosetta.rosetta.core.conformation.ResidueFactory.create_residue(rts.name_map('ACE'))
pose.append_residue_by_jump(lig, 1)

import nglview

WAT is another one like that. There are a couple.

If you have acetyl-lysine, calling the whole residue ALY is the better option —or using the patch `ac`, but from what I gather you have a ligand.

Can you call it XYZ or LIG (with PDB_components off)?

Wed, 2020-08-05 06:44

Thanks! That solved the problem.

Mon, 2020-08-10 08:09