After I had moved to the input_file directory following the Controlling Input and Output in Rosetta,I ran,
$ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb
and I got the output,
-bash: /bin/score_jd2.default.linuxgccrelease: No such file or directory.
What would you recommend doing?
As we don't know exactly where you installed Rosetta on your machine, we have to write the command somewhat generically. The general convention in the documentation and demos is to use "$ROSETTA3" to represent where you have Rosetta installed on your machine. What you'll need to do is manually substitute that with wherever you have Rosetta installed.
For example if you have installed Rosetta on your machine into the directory /home/jgustat/rosetta/Rosetta-3.13/ then when you see a command like
in the documentation, you'll have to make the substitution, such that what you'll actually type in the command line would be
putting in the actual path to the bin directory for the version of Rosetta you have installed on your machine.
(Note the reason we use "$ROSETTA3" is that it works well if you just want to set environment variables. But that's for people who are comfortable with the unix shell - if you don't know how to do that already, I'd recommend just making the substitution yourself, manually.)
I did try to enter it manually instead of using the "$ROSETTA3". I entered the command:
$ env $ROSETTA3=Desktop/Rosetta-jgustat/rosetta_bin_linux_2020.08.61146_bundle/main/source
and it seemed to work, but when I entered:
$ $ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb
I got an error stating that No such file or directory. I tried it with entering it manually and I got the same results.