* Ensure the following files are in the folder you will be working in, 
copy these files from Andy's folder:

LIGAND_NAME.pdb
1WMA_NDP.pdbqt
vina.conf

* Ensure that the terminal directory is in the folder you will be working in:

-- Protonate the ligand of interest:

prodrg LIGAND_NAME.pdb /home/apps/prodrg/prodrg.param CGRP
mv DRGML2.TOPH LIGAND_NAME.mol2; rm DRG*

- yields:

 LIGAND_NAME.mol2

-- Setup MGLTools environment:

source /home/apps/mgltools_x86_64Linux2_1.5.6/bin/mglenv.sh

- should reply "setting PYTHONHOME environment"

-- Ligand PDBQT: 

prepare_ligand4.py -l LIGAND_NAME.mol2 -o LIGAND_NAME.pdbqt

- yields:

 LIGAND_NAME.pdbqt

-- Setup Grid Parameter File (.gpf):

prepare_gpf4.py -l LIGAND_NAME.pdbqt -r 1WMA_NDP.pdbqt -p gridcenter="27.5092,15.8638,1.58914" -p npts="40,40,40" -o 1WMA_NDP_LIGAND_NAME.gpf

- yields:

 1WMA_NDP_LIGAND_NAME.gpf

-- Calculate Grid Maps: 

nohup autogrid4 -p 1WMA_NDP_LIGAND_NAME.gpf -l 1WMA_NDP_LIGAND_NAME.glg &

- yields:

 several .map* files
 nohup.out

-- Setup Docking Parameter File (.dpf):
   *keep pop size >200, evals >5000000, and runs >100 (@200)

prepare_dpf4.py -l LIGAND_NAME.pdbqt -r 1WMA_NDP.pdbqt -p ga_pop_size=200 -p ga_num_evals=5000000 -p rmstol=2.0 -p ga_run=200 -o 1WMA_NDP_LIGAND_NAME.dpf

- yields:

 1WMA_NDP_LIGAND_NAME.dpf

open the .dpf file in an editor (Change unbound_model from extended to bound in the dpf file)
**save over the original .dpf file**

-- Dock:  **this should take several hours**

nohup time autodock4 -p 1WMA_NDP_LIGAND_NAME.dpf -l 1WMA_NDP_LIGAND_NAME.dlg &

hit enter, twice (the & prints to the terminal and runs it in the background (bg))

- yields:

 1WMA_NDP_LIGAND_NAME.dlg

- appends:

 nohup.out

...wait...

-- View docked ligands:

open VMD
File -> New Molecule
browse for 1WMA_NDP_LIGAND_NAME.dlg
change "Determine file type:" to PDB
click Load