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Autodock Tutorial

posted Jun 1, 2011, 8:33 PM by Dong Xu   [ updated Oct 7, 2011, 11:44 AM ]
Docking of mitochondrial respiratory complex II (PDB code: 1ZPO)

/home/apps/ActivePython-2.5.4.4/bin/python /home/apps/pdb2pqr-1.7/pdb2pqr.py --ff=amber --ffout=amber  --with-ph=7.3 --chain 1ZP0_prot.pdb 1ZP0_prot.pqr|tee 1ZP0_prot.pqr.log

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

prepare_receptor4.py -A bonds_hydrogens -U nphs_lps -r 1ZP0_HEM.pdb -o 1ZP0_HEM.pdbqt |tee prepare_receptor4.log

prepare_receptor4.py -U nphs_lps -r 1ZP0_pH73_HEM.2.pdb -o 1ZP0_pH73_HEM.pdbqt |tee prepare_receptor4.log

combine 1ZP0_pH73_HEM.pdbqt

ligand_center.csh 1ZP0_TTF_C.pdb TTF > vina_qp.conf

ligand_center.csh 1ZP0_TTF_D.pdb TTF > vina_qd.conf

prodrg UQ5-2GMH.pdb /home/apps/prodrg/prodrg.param CGRP

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

This line is to show all atom types in ALL ligands, use this info in prepare_gpf4.py step
ls *.mol2.pdbqt|xargs -i cut -c78- {}|awk '! a[$0]++'|sed '/^$/d'|transpose.awk

prepare_gpf4.py -l PA_min.mol2.pdbqt -r 1ZP0_pH73_HEM.pdbqt -p gridcenter="84.348,65.7915,86.1835" -p npts="160,160,160" -p ligand_types="C ,OA,HD,A" -o 1ZP0_pH73_HEM.gpf

nohup autogrid4 -p 1ZP0_pH73_HEM.gpf -l 1ZP0_pH73_HEM.glg &

Vina:

nohup sh -c 'ls *.mol2.pdbqt|xargs -ti vina --config vina_qp.conf --ligand {} --receptor 1ZP0_pH73_HEM.pdbqt --out qp_1ZP0_pH73_HEM--{} --log qp_1ZP0_pH73_HEM--{}.log' >& qd.out &

ls q*.mol2.pdbqt|parallel 'egrep "^REMARK VINA |^ATOM |^HETATM |^MODEL |^ENDMDL" {} > {.}.pdb'

AD4:

Energy:

ls *.mol2.pdbqt|parallel prepare_dpf4.py -l {} -r 1ZP0_pH73_HEM.pdbqt  -p rmstol=2.5 -p ga_pop_size=200 -p ga_num_evals=5000000 -p ga_run=100 -o 1ZP0_pH73_HEM--{.}.dpf

nohup sh -c 'ls *.dpf | parallel autodock4 -p {} -l {.}.dlg' &

ls *.dlg|xargs -ti summarize_docking.py -l {} -t 2.5 -B -a -o summary_of_results_2.5_all

sort -k11g -t, summary_of_results_2.5_all > summary_of_results_2.5_all.sort

Conformation:

ls *.dlg|xargs -ti write_largest_cluster_ligand2.py -f {} -t 2.5 -o {}.pdbqt

ls *.dlg.pdbqt|parallel 'egrep "^REMARK VINA |^ATOM |^HETATM |^MODEL |^ENDMDL" {} > {.}.pdb'
======================================================================
A second example:

  • Re-docking tamiflu (oseltamivir) to N1 neuraminidase protein (2HU4)
  • Setup the receptor/ligand files: wget http://www.rcsb.org/pdb/files/2HU4.pdb

VMD or vi select and export chain B and tamiflu

  • Receptor Protonation: /home/apps/ActivePython-2.5.4.4/bin/python /home/apps/pdb2pqr-1.7/pdb2pqr.py --ff=amber --ffout=amber --with-ph=6.5 --chain 2HU4_chainB.pdb 2HU4_chainB.pqr
  • Ligand Protonation: prodrg G39.pdb /home/apps/prodrg/prodrg.param CGRP ;mv DRGML2.TOPH G39.mol2; rm DRG*
  • Setup MGLTools env: source /home/apps/mgltools_x86_64Linux2_1.5.6/bin/mglenv.sh
  • Receptor PDBQT: prepare_receptor4.py -r 2HU4_chainB.pqr -o 2HU4_chainB.pdbqt
  • Ligand PDBQT: prepare_ligand4.py -l G39.mol2 -o G39.pdbqt
  • Find gridbox center: ligand_center.csh G39.pdb G39
  • Setup Grid Parameter File (.gpf): prepare_gpf4.py -l G39.pdbqt -r 2HU4_chainB.pdbqt -p gridcenter="1.3974,18.7883,108.764" -p npts="40,40,40" -o 2HU4_chainB_G39.gpf
  • Calculate Grid Maps: nohup autogrid4 -p 2HU4_chainB_G39.gpf -l 2HU4_chainB_G39.glg &
  • Setup Docking Parameter File (.dpf): prepare_dpf4.py -l G39.pdbqt -r 2HU4_chainB.pdbqt -p ga_pop_size=200 -p ga_num_evals=3000000 -p rmstol=2.0 -p ga_run=10 -o 2HU4_chainB_G39.dpf  (Change unbound_model from extended to bound in the dpf file)
  • Dock! nohup time autodock4 -p 2HU4_chainB_G39.dpf -l 2HU4_chainB_G39.dlg &

  • Setup config file: center x,y,z and box size (Note the unit is 1A)
  • Dock! nohup time vina --receptor 2HU4_chainB.pdbqt --ligand G39.pdbqt --config vina.conf --out 2HU4_chainB_G39.vina.pdbqt --log 2HU4_chainB_G39.vina.log &
  • Convert PDBQT to PDB: egrep "^REMARK VINA |^ATOM |^HETATM |^MODEL |^ENDMDL" 2HU4_chainB_G39.vina.pdbqt > 2HU4_chainB_G39.vina.pdb


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