I want to cluster the output from a docking study.
However, when running the clustering it complains about my ligand and I get this error message:
----------------------------------------------------------
|ERROR: unrecognized aa lig |
|ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 534 |
----------------------------------------------------------
This is the option file that I've used:
-database /../rosetta_database
-in:file:l list.pdb
-extra_res_fa lig.params
-out:file:silent cluster.out
-run:shuffle
-run:trust_missing_coords
-cluster:radius -1
clustering.py --database=/rosetta-3.2.1/rosetta_database --rosetta=/rosetta-3.2.1/rosetta_source/bin/cluster.linuxgccrelease --pdb_list list.pdb --options=options.cluster summary.txt histogram.txt
How do I get clustering to recognize my ligand?
Thanks,
Yess
Did Rosetta do the docking? Is it the same params file as before? It may be useful to attach the params file and the section of the input PDB where the ligand is to help diagnose the error. It might also be possible that Rosetta is reading in centroid instead of fullatom PDBs; there would have been warnings in the log file if that was the case.
Yes, Rosetta did do the docking and I used the same params as before.
I included the information about the in-file being fullatom (-in:file:fullatom), and that helped! Now the clustering is running, but it doesn't cluster anything.
Parsing pdb file scores
Running cluster
Parsing cluster output
Clusters: 0
Structures: 0
Is there something else that I need to include when clustering a docking study?