Reply To: cluster error

[Anonymous]

The problem with your PDB file is that all your occupancies are zero (columns 54-59). Change column 56 to be 1 instead of 0 (so the occupancies are all 1.00 instead of 0.00) and it will work fine. Rosetta silently ignores zero-occupancy atoms; for these PDBs it silently ignores the entire PDB and crashes down the line.

I believe the flag “-trust_missing_coords” will have the same effect if you don’t want to use a script to fix all your PDB files.