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:

perzik_tassos 113% more lip.fasta >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 -in::file::fasta lip.fasta -database /Xsoftware/rosetta/rosetta_database