Autodock - virtual screening

As I was on a role from my attempts described below I decided to try some virtual screening:

1. I went to the free ZINC database and downloaded a couple thousand molecules.

2. The molecules were downloaded as a single huge .mol2 file which I split using:

split_multi_mol2_file.py -i filename

getting split_multi_mol2_file.py from the AutoDock Virtual Screening Tutorial.

3. Next I converted the mol2 files into pdbqt's using:

foreach f (`ls *`)
echo $f
/home/progs/MGLTools-1.5.1/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py -l $f -d ligand_dict.py
end

4. I divided the pdbqt files into separate directories (of about 1000 compounds) and then carried out the multiple ligand docking pocedure outlined in my posts below. I ran about eight jobs in total on different processors (sort of manual parallel processing!) which took about 24 hours in total processing time.

5. To evaluate the thousands of dockings I ran the script:

#!/bin/csh
cd ./Dockings
foreach d (`/bin/ls`)
echo $d
/home/progs/MGLTools-1.5.1/MGLToolsPckgs/AutoDockTools/Utilities24/summarize_results4.py -d $d -t 2. -L -a -o ../summary_run1.txt
end

This gave me the list:

largestCl_dlgfn #runs #cl #LC LE_LC rmsd_LC #ats #tors
ZINC00000077_rigid/ZINC00000077_rigid, 20, 14, 3, -6.0700, 56.6501, 25, 6
ZINC00000123_rigid/ZINC00000123_rigid, 20, 4, 8, -5.7200, 51.5977, 25, 1
ZINC00000154_rigid/ZINC00000154_rigid, 20, 3, 11, -6.4300, 52.8504, 23, 4
ZINC00000169_rigid/ZINC00000169_rigid, 20, 8, 7, -6.6700, 56.0226, 23, 4

where:

largestCl_dlgfn: filename of the dlg file which contains the result with
the lowest energy in the largest cluster.

#runs: total number of runs found in all the dlg files in the specified
directory

#cl: number of distinct clusters formed in the clustering done on all the
dlg files in the specified directory

LE_LC: the energy of the lowest energy conformation in the largest cluster

rmsd_LC: the rmsd difference between the lowest energy conformation in the
largest cluster and the reference ligand conformation. This is the input
ligand conformation unless a different reference is specified with the
'-f' flag

#ats: number of atoms in the ligand

#tors: number of active torsions in the ligand