* 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
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