Ligand Docking with ARLS

[Anonymous]

I am having troule with the Ligand Docking application. I am currently trying to perform a dock using Automatic RosettaLigand Setup (ARLS). I was able to execute the arls.py script, which creates the arls_work directory. However, once I switch to this new directory, I get an error when I try to run the 1_setup.sh script. Here are the error messages I received:

[XPB33:Rosetta/20160622/arls_work] cameronwilliams% ./1_setup.sh



# Set up directory structure

mkdir -p ligand cofactor unbound input native



# Make ligands

pushd ligand

~/Documents/HDG_Project/Cameron_Work/Rosetta/20160622/arls_work/ligand ~/Documents/HDG_Project/Cameron_Work/Rosetta/20160622/arls_work

mkdir -p {fa,cen}/{conf1,confs,kins,withxtal}



/usr/bin/env python /Applications/rosetta_src_2016.13.58602_bundle/main/source/src/apps/public/ligand_docking/molfile_to_params.py -c -nX00 -pHx -kHx.kin /Users/cameronwilliams/Documents/HDG_Project/Cameron_Work/Rosetta/20160622/Hx.mol2 && cat Hx_????.fa.pdb | gzip -c > fa/withxtal/Hx_confs.fa.pdb.gz && ( [ -f Hx_0002.fa.pdb ] || cp Hx_0001.fa.pdb Hx_0002.fa.pdb ) && mv Hx_0001.fa.pdb fa/conf1/ && cat Hx_????.fa.pdb | gzip -c > fa/Hx_confs.fa.pdb.gz && mv Hx_????.fa.pdb fa/confs/ && echo 'PDB_ROTAMERS Hx_confs.fa.pdb' >> Hx.fa.params && cp Hx.fa.params fa/withxtal/ && mv Hx.fa.params fa/ && mv Hx.fa.kin fa/kins/ && cat Hx_????.cen.pdb | gzip -c > cen/withxtal/Hx_confs.cen.pdb.gz && ( [ -f Hx_0002.cen.pdb ] || cp Hx_0001.cen.pdb Hx_0002.cen.pdb ) && mv Hx_0001.cen.pdb cen/conf1/ && cat Hx_????.cen.pdb | gzip -c > cen/Hx_confs.cen.pdb.gz && mv Hx_????.cen.pdb cen/confs/ && echo 'PDB_ROTAMERS Hx_confs.cen.pdb' >> Hx.cen.params && cp Hx.cen.params cen/withxtal/ && mv Hx.cen.params cen/ && mv Hx.cen.kin cen/kins/

Traceback (most recent call last):

File "/Applications/rosetta_src_2016.13.58602_bundle/main/source/src/apps/public/ligand_docking/molfile_to_params.py", line 26, in <module>

from rosetta_py.io.mdl_molfile import *

ImportError: No module named rosetta_py.io.mdl_molfile



popd

~/Documents/HDG_Project/Cameron_Work/Rosetta/20160622/arls_work



# Make cofactors

pushd cofactor

~/Documents/HDG_Project/Cameron_Work/Rosetta/20160622/arls_work/cofactor ~/Documents/HDG_Project/Cameron_Work/Rosetta/20160622/arls_work

mkdir -p {fa,cen}/{conf1,confs,kins,withxtal}





popd

~/Documents/HDG_Project/Cameron_Work/Rosetta/20160622/arls_work



# Make "unbound" proteins (never prepacked, never a ligand or cofactor)

cp /Users/cameronwilliams/Documents/HDG_Project/Cameron_Work/Rosetta/20160622/HDG.pdb unbound/HDG.pdb



# Make native and input PDBs, with ligands and cofactors

# May later be replaced by repacked PDB files

cat /Users/cameronwilliams/Documents/HDG_Project/Cameron_Work/Rosetta/20160622/HDG.pdb  ligand/fa/conf1/Hx_0001.fa.pdb > native/HDG_Hx.pdb

cat: ligand/fa/conf1/Hx_0001.fa.pdb: No such file or directory

cat /Users/cameronwilliams/Documents/HDG_Project/Cameron_Work/Rosetta/20160622/HDG.pdb  ligand/fa/confs/Hx_0002.fa.pdb > input/HDG_Hx.pdb

cat: ligand/fa/confs/Hx_0002.fa.pdb: No such file or directory

 

[Anonymous]

ARLS and the ligand docking application are relatively old. They’re somewhat deprecated. Instead, you should probably be using the ligand docking protocol from DeLuca et al. (http://dx.doi.org/10.1371/journal.pone.0132508). See also the demo in the Rosetta repository, under Rosetta/demos/protocol_capture/rosettaligand_transfom, or https://www.rosettacommons.org/demos/latest/protocol_capture/rosettaligand_transform/README

Unfortunately, there really isn’t a nice bulk-docking automation script to automate the process. If you have multiple ligand you’d have to do the scripting yourself.

The proximal cause of your problem, though, is that the /Applications/rosetta_src_2016.13.58602_bundle/main/source/scripts/python/public/ directory isn’t in your PYTHONPATH. We reorderd the script directories since arls.py was written, and the auto setup magic that it did apparently no longer works quite right. — You should be able to add the path to the PYTHONPATH environment variable yourself, though.

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