I am attempting to run the AbinitioRelax application and when I use the -abinitio:relax option it returns an error.
Here are my commands: /home/xxxx/Documents/rosetta/main/source/bin/AbinitioRelax.default.linuxgccrelease @flags
where flags file contains:
I then get an error:
not found in command line top-level context
Did you mean:
Does anyone have any suggestions? I am rather stuck at this point as the source code contains the relax option for abinitio.
The first thing I'd check is if you have `-relax` by itself somewhere (versus the full `-abinitio:relax`) -- That's the sort of error message you see when you have a option (like `-relax`) without any of the parent categories, and where the option is ambigious.
The second thing I might try is running the options file through the `dos2unix` program. DOS-style line endings (used with Windows) have extra characters which mess up programs (like Rosetta) expecting Unix-style line endings.
A third thing to try is to remove any blank lines in the options file. This is a bit of a long-shot. I'm a little confused as to why the option which was not found in top level context is not being printed. I'm wondering if it might be because there's some issue with a blank line throwing the options parser. (It should be okay with blank lines, and I'm not sure where the relax is coming from, but if nothing else seems to be working, that might be worth a shot.)
As a final test, you can try re-typing (don't copy/paste!) the options into a new text file using your favorite Mac/Unix (not Windows) plain-text editor (not a word processor). `gedit` and `nano` are popular ones if you're not familiar with `vim` or `emacs`. The rationale behind this is that there may be some non-printing character or extended-set character in the option file which is messing things up. By retyping in a plain-text editor, you avoid inserting any such characters.