Autodock 4 - making gpf & dpf files

I made my grid parameter files using Autodock tools, with the atom types found in the top of summary.txt from my ligands directories (simply add the atom types to the pop-up box in ADT) as per the tutorial. I ran AutoGrid and then checked to make sure I had all the .map files I was expecting.

Next I copied all of my ligand pdbq files into the same directory as my grid files. I then ran the following script, adapted from the virtual screening tutorial:

#!/bin/csh
mkdir Dockings
cd Dockings
foreach f (`ls ../*.pdbqt`)
set name = `basename $f .pdbqt`
echo $name
mkdir "$name"_rigid
cd "$name"_rigid
cp ../"$f" .
ln -s ../../protein.pdbqt .
ln -s ../../protein*map* .
/home/progs/MGLTools-1.5.1/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py -l `basename $f` -r protein.pdbqt \
-p ga_num_evals=1750000 \
-p ga_pop_size=150 \
-p ga_run=20 \
-p rmstol=2.0
mv "$name"_protein.dpf "$name"_rigid.dpf
cd ..
end

This made a new directory called "Dockings", within this a directory for each of my ligands, and within each ligand directory a link to the appropriate map files and a docking parameter file for the AutoDock run for each ligand.

To run the multiple autodockings I made a file called ligands.list containing the name of all my ligand directories (ls > ligands.list then delete the file names) and invoked multiple autodock runs with:

#!/bin/csh
foreach d (`cat docking.list`)
echo $d
cd $d
/home/progs/AutoDock/autodocksuite/bin/i8664Linux2/autodock4 -p $d.dpf -l $d.dlg
cd ..
end