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Andy Coombs' Tutorial on 1WMA Docking

posted Jan 27, 2012, 10:58 AM by Dong Xu   [ updated Jan 27, 2012, 11:01 AM ]
* 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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