Docking_Scripts

Contributors: Javier Baylon, Andres Arango, Archit Vasan

Required softwares

First, download autodock vina, and adtools.

vina: http://vina.scripps.edu adtools: http://autodock.scripps.edu/resources/adt

Steps

0. • make pdbqt file of ligand, starting from the pdb file (this can be done with adtwools).
     Run make_ligand_pdbqt. THis puts pdbqt file into pdbqt.ligand
1. • get snapshots of the protein from simulations trajectory, using get_frames_for_pdbqt.tcl, then fix using 'set.element.tcl'.
2. • make receptor pdbqts using 'make_receptor_pdbqt'. this step takes a while, you can start creating a small number of frames just to get an idea of how it works.
3. • make conf files for autodock vina, using 'make_confs' scripts. you will need to change the name of ligand to match whatever your ligand pdbqt is called.
4. • run docking using autodick vina - the main line is :

   path_to_autodock_vina/vina --config conf.files/$JOBNAME.conf --cpu $NCPUS Just run run_docking.sh and this should be taken care of

5. • get ligand binding poses from the generated log files using 'get_pdb_from_dlg', this will generated pdbs that can be visualized in vmd!
6. • merge protein and ligand together using merging_poses.tcl
7. • load merged files to vmd using vmdload.tcl
8. • optionally, after loading in vmd, create a js file with all docked poses... this should decrease the time it takes to load.
9. • save list of energies using get_energies.sh