The enzyme_design application is one of those applications which has not been transitioned to the “jd2” input/output/job distribution framework, so the controls for input/output can be limited and idiosyncratic. As I read the code, there isn’t any facility to output enzyme design structures as a silent file with the enzyme_design applications.
Note that if you really wanted silent file output, you could put together an enzyme design protocol in RosettaScripts, probably relying heavily on the enzyme design movers ( https://wiki.rosettacommons.org/index.php/Movers_%28RosettaScripts%29#Enzyme_design ). rosetta_scripts is a jd2 application, so it is able to handle all the standard input and output flags. Some caveats, though. If you’re using enzdes-style constraints, you need to use the -run:preserve_header flag to keep Rosetta from discarding the constraint-specifying REMARK lines. Also, if you’re using silent files, you want to make sure you’re using the “binary” formatted silent file (with the silent_struct_type flags), as the default “protein” silent file can’t handle ligands well. I’m also not sure if using enzdes style constraints with silent files is even possible, as I don’t know how good the REMARK-preserving behavior of silent files is.
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