I'm trying to use the partial_thread application to fill in some gaps in a PDB crystal structure, 2hko. This structure has an FAD ligand and a key water I'm trying to keep during threading. I've cleaned the file as recommended, changed the FAD ligand atom types to match the canonical Rosetta atom types, and made similar changes to my water. While the threading runs, the ligand gets thrown out.
This is the command I used:
partial_thread.static.linuxgccrelease -database $ROSETTA_HOME/main/database -in:file:fasta lsd1.fasta -in:file:alignment alignment.aln -in:file:template_pdb 2hko_cleaned.pdb -verbose
I'm pretty new to Rosetta so please bear with me! Thanks,