I have the following flags in my refinement flag file, I'm getting the error ERROR: Unused "free" argument specified: GDP.fa.tors, I'm not sure why!
-extra_res_cen GTP.cen.params GDP.cen.params -extra_res_fa GTP.fa.params GDP.fa.params-extra_improper_file GTP.fa.tors GDP.fa.tors
If that's your actual command line, you're missing a space between GDP.fa.params and -extra_improper_file.
First off, you're missing the space between the GDP.fa.params and the -extra_improper_file
Secondly, the different options in an options file need to be on different lines. Because you're starting a line with "GTP.fa.tors" it's trying to recognize it as an option, rather than a parameter to the -extra_improper_file option. Your options file should look more like the following. (Including the line breaks)
Ok, here's my full script. It's funny now I'm getting a different error below.
core.import_pose.import_pose: [ ERROR ] File: /home/labusr/Documents/starting_single_dimer.pdb not found!
Your argument to -s is wrong. If the file exists it's possible you don't have permission to read it.
Thanks a lot it's running now in a bash script, but I'm trying to call these commands using subprocess.call in Python. Here's my Python script. I'm still getting unused free argument there:
Edit: never mind what I said above. It's not working, this is what Igot at the end of the log:
This is a python or other script error not a Rosetta error.
It's not clear to me why `./A_asymm_refine.sh` is mentioned in the log file as it does not appear in the python snippet you have posted. I assume you have a shell script calling a python script calling Rosetta and you have loose junk in the outermost shell script A_asymm_refine.
If you are sure this is in python - I would preformat your argument to subprocess.call as one big string and print it, to ensure it comes out right and that you don't have any loose endline characters in it from your variable substitutions.
First, I want to debug the bash script, becasuse it doesn't seem to be working! It initially runs fine, then gives these errors ./"name of script".sh: line 14: "flag": command not found. I attached the script, it's better to inspect it to verify the syntax is correct. Thanks a lot, I appreciate your help.
Bash needs all the arguments on one logical line. Notice most of your arguments end in \. Those \ are escaping the newline character so that bash interprets it all as once logical line even though it prints on multiple lines. Then notice some of the lines - the ones causing problems - are missing their trailing \. The last line should not have a \ as it is really the end of a line and thus should have an endline character.
Fantastic, now after fixing that stuff (sorry I'm familiar with python more than bash), I get the same error as in the python script (which makes more sense):
I contacted Frank, he told me to cat the two files. Thanks a lot for all of your help.
I've never used -extra_improper_file. If you look at the options documentation you will find https://www.rosettacommons.org/docs/latest/full-options-list that it takes a string, not a stringVector - in other words you are allowed only one file argument here, not arbitrarily many (like for extra_res_fa).
If you need multiple of these files - you can probably concatenate them together. You might need to delete the header in the second one to do that. You might also need to manually resolve any duplicates.