Rosetta

There is a locally installed version of Rosetta at our Linux cluster.

My current way of doing things is:

Go first to [1] There you submit your sequence to create the fragments needed to run later locally the AbRelax protocol for ab initio folding. I choose to that remotely since its too cumbersome to fully install it locally, and its pretty quick.

Then make a new directory with you sequence in FASTA format, eg:

>our lipase
MRAPIPEPKPGDLIEIFRPFYRHWAIYVGDGYVVHLAPPSEVAGAGAASVMSALTDKAIV
KKELLYDVAGSDKYQVNNKHDDKYSPLPCSKIIQRAEELVGQEVLYKLTSENCEHFVNEL
RYGVARSDQVRD

The job gives two files, accessible after completion through the 'download' button.

• _03_*
• _09_*

You need these files copied to your run directory for the big job ...

And then you need something like this

/Xsoftware/rosetta/rosetta_source/bin/AbinitioRelax.linuxgccrelease 
  -abrelax -abinitio:relax 
  -in::file::fasta lip.fasta 
  -database /Xsoftware/rosetta/rosetta_database 
  -in:file:frag3 aat000_03_05.200_v1_3 
  -in:file:frag9 aat000_09_05.200_v1_3 
  -out:pdb -out:path PDB_files_run1 -out:file:silent abrelax_silent