1) I am running the protocol for comparative modeling, and run the program it tells not find some flags. The question is, is this common? It will really interfere too much in my final result?
2) what the function of this sequence, after calling the program? (@flags >& test.log &)
ERROR: Option matching -silent_decoytime not found in command line top-level context
caught exception ERROR: Option matching -silent_decoytime not found in command line top-level context
1) The -silent_decoytime option was removed from Rosetta about a year ago. - What it was supposed to do was to "Add time since last silent structure was written to score line", but it actually wasn't doing anything - there wasn't any place in the code which actually looked at the value of the option.
So it should be safe to just remove that option from the commandline or the options file.
2) The "@flags >& test.log &" bit is actually doing three different things:
Thank you very much RMORETTI.