Error when trying docking protocol with different ligand

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    • August 5, 2020 at 11:37 am #3532
      Anonymous

        Hi,

        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/PoseFromSFRBuilder.cc:342

        [ 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.

        Thanks,

        Emzo

      • August 5, 2020 at 1:44 pm #15431
        Anonymous

          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
          
nglview.show_rosetta(pose)

          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)?

          • August 10, 2020 at 3:09 pm #15442
            Anonymous

              Thanks! That solved the problem.

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