I am currently using enzdes to design non-enzymatic protein-ligand interfaces. When invoking this protocol, I have been struggling to generate both silent output files and score files that contain the full array of metrics (scorefiles that contain the SR* columns). From what I have read online, the -out::file::o <filename> option is required to generate the SR* metrics. However, when this is invoked, the ouput structures are pdb files and not silent files, and I do not have the space to output pdbs on large scale runs. Additionally, if I do not provide this option, I receive the silent file, but the score file does not contain the SR* columns and this warning is printed:
WARNING: The following options have been set, but have not yet been used:
Is there a way I can both generate silent files and score files with SR* metrics? I believe it requires having the -jd2:enzdes_out option invoked without invoking -out::file::o <filename>, but I have not found a way to do this. I have attached two log files and a combined score file. Files/scores with the extention _devNull are from a run where a silent file and incomplete scorefile were generated. Files/scores with the extention _devNullnoSilent are from a run where a pdb and complete scorefile were generated.
Any insight into this would be greatly appreciated.
The -jd2:enzdes_out option is specifically for PDB output with the scorefile. If you specify silent file output you'll skip that entirely.
Generally speaking, silent files aren't used with score files -- it's rather redundant, as the scorefile information is in the silent file. (Technically speaking, a scorefile is just a type of silent file without any structural information.)
Instead, what you can do is run 'grep SCORE silent.out' on your silent file after the run completes, and that should contain all the scoring information that would have been in the scorefile, without any of the structural information.