Ligand Tutorial

Example: HIV-1 Protease Inhibitor, XK-263

This example shows how to use the ADT interface to Ligand to format a small molecule, in this case, an HIV-1 Protease Inhibitor, XK-263. The following sections describe each of the menu options in the Ligand module.

Ligand :

Input Molecule

Read Molecule

as shown below, this opens a file browser to facilitate selecting the ligand. Notice these things about this type of file browser:
Clicking on the bar at the right of the 'Files of type:' button shows a list of alternative file types. Currently the browser is listing files of type 'pdbq'. A 'mol2' or 'pdb' file type could be selected here.
Activate current choice by clicking on 'Open' button or 'Return' keystroke.
NB: All atoms in the molecule must have their valencies are completed and partial charges added. Ligand adds polar hydrogens and charges of either Kollman or gasteiger type. The total charge on each 'residue' in the ligand must be an integral value. Ligand checks the total charges and notifies the user if there is a problem. The user must edit the final output file to correct any charge error. (In the case of non-peptide ligands, all the atoms in the ligand are grouped into one residue by the Molecule Viewer's parsers.)

Choose Molecule

use this option when the molecule has already been read in to the viewer.

Rigid Molecule

Selecting xk.pdbq results in displaying this molecule in the Viewer and in setting a number of Ligand specific values stored in a dictionary, `mv.atorsDict'.

Ligand :

Define Rigid Root

Autotors formats the ligand file inserting keywords based on the metaphor of a tree. The 'root' is defined as the fixed portion of the ligand, from which rotatable 'branches' sprout. Branches within branches are possible. Nested rotatable bonds are rotated in order from the 'leaves' to the 'root'. The 'root' is set either to an atom picked by the user or automatically to the atom which is considered to be in the center of the molecule with the most 'balanced' subtrees. The root atom is marked in adt by a large green sphere. [Please note here that the visibility of this sphere may be toggled on and off via the last menu entry in the Ligand menu: 'hide sphere(s) marking root atom(s)']

By Picking

The user sets the root to a vertex by 'picking' it with the left-mouse button. In the image below, the user has selected C7 as the root atom.

Automatically

AutoRoot detects which atom in the molecule has the smallest 'largest-subtree'. (for more details, see reference manual)

Show Root Atoms

atoms contiguous with the picked atom up to the first 'active' torsion are considered part of the 'root' by Ligand. Visualizing this expansion consists of marking adjacent root atoms with small green spheres. The user may toggle this visualization on and off.

Ligand :

Define Rotatable Bonds

To allow flexibility in the ligand, AutoDock can handle up to MAX_TORS torsions, which is set to 32 but can be changed by recompiling the AutoDock source code. Bonds in cycles and bonds to 'leaf' atoms are not able to be flexible in AutoDock. All other bonds could be. This portion of Ligand consists of deciding which of the possible torsions to model as flexible.
During this phase, bonds are color-coded to show which cannot be flexible: colored red, which are currently active: colored green and those which could be active but have been inactivated by the user: colored purple. Labels for atoms in bonds which could be flexible are composed of the atom name and its number.
A separate toplevel widget, 'Torsion Count', facilitates these actions. It includes a display of the total number of currently active torsions, buttons to Disallow Peptide Backbone Torsions' and 'Disallow Amide Torsions' and a button to stop labelled 'Done'. The total number of current active torsions is displayed. Inactivations in this phase are reversible.
When the user is finished defining rotatable bonds, he clicks 'Done' which closes the 'Torsion Count' widget, restores the display and removes the labels.

Ligand :

Aromatic Carbons :

Calculations based on the force field used in AutoDock treat planar carbons differently from aliphatic carbons. For this reason, Ligand checks carbons in rings for planarity. Here, aromaticity is an all or none property: if some atoms in a ring fail the aromaticity cut-off, none of the carbons in that ring are considered aromatic.
Rename Aromatic Carbons

Carbons in cycles in which all atoms are found to be planar are marked aromatic by changing their names to 'A...'. They are colored green in the Viewer and their element type is set to 'A'.

Restore Aliphatic Carbons

Names, colors, and elements are restored for planar ring carbons.

Set Carbon Names

Individual carbons may be picked, arbitrarily changing their name and display color.

Change Aromaticity Criteria

The aromaticity cut-off is set to 7.5 degrees between the normals to adjacent carbon atoms in a ring. This value may be changed by the user.

Ligand :

Non Polar Hydrogens

The united atom model simplifies a docking by reducing the overall number of atoms to be considered. This is accomplished by merging nonpolar hydrogens with the carbons to which they are bonded. The partial charge of each non-polar hydrogen is added to the charge of its carbon and then the hydrogen is 'eliminated' from the molecule. In the viewer, the bonds between the carbons and their hydrogen neighbors are removed as are the hydrogen atoms themselves.

Ligand :

Write PDBQ ... :

In writing the formatted output file, the convention is to name this new file with the extension 'out.pdbq'. Here we wrote xk.out.pdbq. This file contains the necessary keywords to mark ROOT and BRANCH parts of the ligand. Please note, Ligand changes the order of the atoms in the output file because they are written starting with the root atoms and followed by the rest as encountered in a breadth-first order traversal of the branches. The atoms are renumbered. Non-polar hydrogen atoms are not written if they are merged when output file is produced. If cyclic carbons have been converted to aromatic type, their names will reflect this change. The next output line contains another important keyword, TORSDOF, which is is the number of torsional degrees of freedom initially detected for the molecule (and is not changed by toggling torsions). The first lines in the output file include information for AutoDock about the flexibility of the torsions and begins with the keyword 'REMARK'. CONECT records are written at the end of the file.

Ligand :

Show Ligand rootSpheres

Visibility of the large green sphere which marks the current root atom and the smaller ones which mark root expansion can be changed with this menu entry.

Ligand :

Automatic autotors setup

This option allows the user to prepare a ligand for AutoDock in one step, assigning charges, possibly merging non-polar hydrogens, lone pairs and disallowing amide and peptide-backbone torsions. This feature is particularly useful in scripts.

ADT

Introduction

Ligand

Grid

Docking

Run

Analyze