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Ligand Docking with ARLS

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Ligand Docking with ARLS

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 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 script. Here are the error messages I received:

[XPB33:Rosetta/20160622/arls_work] cameronwilliams% ./ 

# 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/ -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/", line 26, in <module>
    from import *
ImportError: No module named


# 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}


# 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


Post Situation: 
Thu, 2016-06-23 09:34

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. ( See also the demo in the Rosetta repository, under Rosetta/demos/protocol_capture/rosettaligand_transfom, or

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 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.

Thu, 2016-06-23 10:55