I'm trying to use the ddg_monomer application as described in the rosetta3.3 manual. It gives a command for preminimization of your input pdb structure using the application "minimize_with_cst". Trying this exact code with my pdb, or even with 2ci2.pdb found with the integration test, ends with "using -l option" as the last line of the output. Anyone else having similar problems or have a solution?
Also, the actual ddg_monomer application with 2ci2.pdb DOES work for me correctly.
The only way I can see that the minimize_with_cst application can exit without crashing with a last line of "using -l option" is if the list file you pass with -l is empty. (The list file should contain a whitespace (e.g. carriage return) separated list of structure files to read in.)
Is the program successfully exiting or is it crashing? If you're redirecting the output (e.g. the "> mincst.log" bit), when the program crashes it is possible that not all of the output actually gets written to the log file. Try running it in the terminal without redirection and see if there's more program output.
Thanks rmoretti, but redirection didn't help. After help from the developer, it turns out that saving the list with a .txt extension was the problem. Simply make the list using a shell command of: ls *.pdb > listname
After that the application worked fine.