I'm trying to run AbinitioRelax on a cluster (remotely), but I keep getting the error that there is no such file or directory when the executable tries to release. My command is as follows:
../../rosetta_source/src/apps/public/AbinitioRelax.linuxgccrelease -database ../../rosetta_database -in:file:fasta ./"Rosetta files"/pin.fasta in:file:frag3 ../"Rosetta files"/aat000_03_05.200_v1_3 -in:file:frag9 ../"Rosetta files"/aat000_09_05.200_v1_3 -abinitio:relax -relax:fast -abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -abinitio::rsd_wt_helix 0.5 -abinitio::rsd_wt_loop 0.5 -user_filters true -psipred_ss2 ../"Rosetta files"/t000_.psipred_ss2 -kill_hairpins ./input_files/1elwA.psipred_ss2 -out:pdb pin.pdb -nstruct 10
I adapted the paths to the input files as necessary and changed the output to pdb instead of silent. Otherwise, this is pretty much verbatim the set of "optimal performance" commands as given in the documentation on the AbinitioRelax page. I ran both the /../../bin/AbinitioRelax.linuxgccrelease (as presented in the documentation) and what is shown above, since that was what was given as the path to the executable in the documentation's text. I'm executing from the Rosetta home directory (if you ls you see all the main directories, as well as the directory to my input files). What's wrong with my picture? I'm fairly new at linux, and even newer at using suites like these, so if the error is trivial and obvious, apologies.