I am using a RosettaScripts which outputs structure coordinates to a database (.db3). I am trying to extract the individual PDB files. I tried using the following command:
score_jd2.static.linuxgccrelease -inout:database_filename struct.db3
as suggested here https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/sql/Rosetta-Database-Output-tutorial. But it gives an error:
ERROR: Option matching -inout:database_filename not found in command line top-level context
caught exception ERROR: Option matching -inout:database_filename not found in command line top-level context
Any idea of what I can do to fix this?
In case you need more info, the RosettaScript XML I am using is in the supplementary materials to this paper: https://www.biorxiv.org/content/early/2017/11/17/221689