Question about motif + ligand scaffolding

[nicolasrincont]

Dear all. I'm trying to design an enzyme with the following config:
motif1_pc:
source: ame_targets
target_filename: motif1_pc
ligand: "L:1"
contig_atoms: "B11: [CD, OE1, OE2]; B15: [CE, NZ]; B16: [CB, OG1]; B18: [CG, OD1, OD2]; B23: [CD, OE1, OE2]"
binder_length: [180]
hotspot_residues: [null]
target_path: ./assets/target_data/ame_input_structures/motif1_pc.pdb
use_bonds_from_file: True
I generated 1000 thousand designs and all of them have INF for the ligand scRMSD. I wonder if you have any ideas or suggestions about what can be modified so that the ligand goes to the desired location.

[nvdreidenbach]

Can you upload the target file?

[nicolasrincont]

Can you upload the target file?

motif1_pc.pdb

[nvdreidenbach]

I believe the ligand should only have heavy atoms. Another issue could be if you are asking for a partial side chain not defined by the AME task.

If you’re still getting errors I’d suggest stepping through the read calculation and sharing the model generated pdb to see what is happening with the ligand

[nicolasrincont]

I believe the ligand should only have heavy atoms. Another issue could be if you are asking for a partial side chain not defined by the AME task.

If you’re still getting errors I’d suggest stepping through the read calculation and sharing the model generated pdb to see what is happening with the ligand

I'll try removing the hydrogens. I'm not sure what you mean with a partial side chain not defined by the AME task.

Here is the log of the generation and the pdb of the model with the lowest scRMSD for the binder. The ligand is there but it isn't located close to the motif residues:

complex_job_0_n_180_id_892_single_orig12_mpnn_fixed_seq0_complex_model.pdb
generate.log