Day 3: Design‎ > ‎

ligand & symmetry tutorial

This tutorial gives you an example of how to handle symmetry and ligand in RosettaRemodel

first, let's start from the home directory
cd ~

Then we download from this website all the files in the altronate_ligand_files, and move the file to the new directory and unzip it
mv ~/Downloads/altronate_ligand_files.zip .
unzip altronate_ligand_files.zip

The directory contains all the necessary files for this tutorial.  now go into the directory
cd altronate_ligand_files

We pre-generated the files for you, but you normally would have to go through all the steps of preparing the pub file for rosetta first.  The ligand params file is needed for this step, so that has to be done first.  then you relax the structure:
rosetta_scripts.default.linuxgccrelease @repack.options -s 2hxu_renum.pdb -parser:protocol repack.xml -extra_res_fa LG.fa.params

After that is done, first you need to create the ligand params file and symmetry file for the protein we are interested in
perl ~/Rosetta/source/src/apps/public/symmetry/make_symmdef_file.pl -m PSEUDO -a A -b B -p 2hxu.pdb > ALT.symm

We'll look through the files with explanation and eventually run
~/Rosetta/source/bin/remodel.linuxgccrelease -s 2hxu_renum.pdb -remodel:blueprint test.bp -remodel:use_cart_relax -extra_res_fa LG.fa.params -extra_res_cen LG.cen.params -overwrite -enzdes:cstfile cst_harley -num_trajectory 1 -score:set_weights pro_close 0  -remodel:free_relax -no_optH false -symmetry_definition ALT.symm -max_linear_chainbreak 2 -ex1 -ex2 -ex3 -ex4 -beta -cstfilter 150 -jd2:no_output  -out:prefix sym_free

A random output file generated from this command is attached here (use the link below).  You can compare the 2hxu_renum.pdb and the sym_free_1.pdb to see what RosettaRemodel did. 

ċ
sym_free_1.pdb
(1393k)
Unknown user,
Oct 14, 2016, 9:49 AM
Comments