Using AutoDock 4 and Vina

with AutoDockTools:
A Tutorial

Written by Ruth Huey, Garrett M. Morris and Stefano Forli

The Scripps Research Institute

Molecular Graphics Laboratory
10550 N. Torrey Pines Rd.
La Jolla, California 92037-1000
USA

8 December 2011

1
Contents

USINGAUTODOCK4 ANDVINAWITHAUTODOCKTOOLS:
A TUTORIAL................................................................................... 1
Written by Ruth Huey, Garrett M. Morris and Stefano Forli
.............................................................................................................................1
The Scripps Research Institute
Molecular Graphics Laboratory
10550 N. Torrey Pines Rd.
La Jolla, California 92037-1000
USA ....................................................................................................................1
8 December 2011
.............................................................................................................................1

Contents..........................................................................2

Introduction.....................................................................4

FAQ – Frequently Asked Questions.....................................5

Overview: What is a Docking?............................................7

AUTODOCK Procedure:.................................................................7
VINA Procedure:.........................................................................11

Exercise One: PDB Files Are Not Perfect: Editing a PDB File
......................................................................................13
Procedure:..................................................................................14

Exercise Two: Preparing a Ligand for AutoDock................16

Procedure:..................................................................................16

Exercise Three: Preparing the Macromolecule. ................20

Procedure:..................................................................................20

Exercise Four: Preparing the Grid Parameter File. ...........21

AUTODOCK Procedure:...............................................................21

Exercise Five: Starting AutoGrid 4...................................24

Procedure:..................................................................................24

Exercise Six: Preparing the Docking Parameter File. ........26

Procedure:..................................................................................26

Exercise Seven:Starting AutoDock4/AutoDockVina...........28

AUTODOCK4 Procedure:.............................................................28
VINA Procedure:.........................................................................29

2
Files for Exercises:..........................................................30
Input Files:.................................................................................30
Results Files...............................................................................30
Ligand.............................................................................................................. 30
Macromolecule.................................................................................................30
AutoGrid.......................................................................................................... 30
AutoDock......................................................................................................... 30
VINA................................................................................................................30

Appendix 1: PMV Basics..................................................31

Modifier........................................................................................................31
Pick.......................................................................................................... 31
Rotate.......................................................................................................31
Shift.............................................................................................................. 31
Key............................................................................................................... 31
R..........................................................................................................31

Appendix 2: Dashboard Widget........................................33

Appendix 3: Conformation Player ....................................35

Appendix 4: Docking Parameters.....................................40

Parameters common to SA, GA, GALS:.......................................40
Simulated Annealing Specific Parameters:.................................43
Genetic Algorithm Specific Parameters:.....................................44
Local Search Specific Parameters:.............................................45
Clustering Keywords:..................................................................46

3
Introduction

This tutorial will introduce you to docking using the AutoDock suite
of programs. We will use a Graphical User Interface called
AutoDockTools, or ADT, that helps a user easily set up the two
molecules for docking, launches the external number crunching jobs in
AutoDock, and when the dockings are completed also lets the user
interactively visualize the docking results in 3D.
FAQ – Frequently Asked Questions

1. Where should I start ADT?

You should always start ADT in the same directory as the

macromolecule and ligand files. You can start ADT from the
command line in a Terminal by typing “adt” and pressing
<Return> or <Enter>.

2. Should I always add hydrogens?

Yes, for both the macromolecule and the ligand, you should
always add hydrogens, compute Gasteiger charges and then
you must merge the non-polar hydrogens. Polar hydrogens are
hydrogens that are bonded to electronegative atoms like
oxygen and nitrogen. Non-polar hydrogens are hydrogens
bonded to carbon atoms.

3. How many AutoGrid grid maps do I need?

You need one AutoGrid map for every atom type in the ligand
plus an electrostatics map and a desolvation map. E.g.: for
ethanol, C2H5OH, you would need C, OA and HD maps plus an
electrostatics ‘e’ map plus a desolvation ‘d’ map.

4. Why should all the total charges on the residues be an integer?

This is because it is assumed that the residue is interchangeable

with others, and that no electrons are withdrawn or received by
adjacent residues. In proteins, e.g., arginines should have a
total charge of +1.000 if they are protonated, or 0.000 if they
are neutral.

5. How easy will it be to get good docking results?

In general, the more rotatable bonds in the ligand, the more

difficult it will be to find good binding modes in repeated
docking experiments.
6. How big should the AutoGrid grid box be?

The grid volume should be large enough to at least allow the

ligand to rotate freely, even when the ligand is in its most fully-
extended conformation.

7. Can I identify potential binding sites of a ligand on a protein

with AutoDock?

Yes, if you do not know where the ligand binds, you can build
a grid volume that is big enough to cover the entire surface of
the protein, using a larger grid spacing than the default value of
0.375Å, and more grid points in each dimension. Then you can
perform preliminary docking experiments with AutoDock to
see if there are particular regions of the protein that are
preferred by the ligand. This is sometimes referred to as
“blind docking”.

Then, in a second round of docking experiments, you can build

smaller grids around these potential binding sites and dock in
these smaller grids.

If the protein is very large, then you can break it up into

overlapping grids and dock into each of these grid sets, e.g. one
covering the top half, one covering the lower half, and one
covering the middle half. The third-party tool, BDT, automates
this process; see http://autodock.scripps.edu/resources.
 Overview: What is a Docking?

An AutoDock search for the best ways to fit two molecules together
constitutes a docking. The docking consists of a series of independent
searches or runs which results in a final ‘pose’ or conformation of the
ligand. Each conformation is the lowest energy found during a search.
An AutoDock experiment generally includes clustering of
conformations based on their similarity. The two molecules to fit
together and which search method to use are specified in the docking
parameter file (DPF). The results are written to a docking log file
(DLG). Reading a docking log or a set of docking logs into ADT is
Note: the dlg file contains many details that
the first step in analyzing the results of docking experiments.
are output as AutoDock parses the input files
and reports what it finds. For example, when In this exercise we will use the file imatinib_1iep_receptor.dlg from
AutoDock opens each AutoGrid map, it
reports opening the map file and how many a previous AutoDock calculation. In it, the imatinib (Gleevec ©
data points it read in. When it parses the input Novartis), a drug mainly used for the treatment of chronic
ligand file, it reports building various internal
data structures. After the input phase, myelogenous leukemia (CML), is docked to the c-Abl kinase domain.
AutoDock begins the specified number of The key results in a docking log are the docked conformations found at
runs. It reports which run number it is
starting; it may report specifics about each the end of each run, the energies of these docked structures and their
generation or simulated annealing cycle. similarities to each other. The similarity of docked structures is
After completing the runs, AutoDock begins
an analysis phase of the conformational measured by computing the root-mean-square-deviation, rmsd,
similarity of the dockings. At the very end, it between the coordinates of the atoms and creating a clustering of the
reports a summary of the time taken and
outputs the words ‘Successful Completion’. conformations based on these rmsd values.
The level of output detail is controlled by the
parameter “outlev” in the docking parameter
file. For dockings using the LGA algorithm, A visual examination of the interactions between the docked ligand
minimal output (‘outlev 0’) is recommended. and the macromolecule is used to evaluate the chemical
reasonableness of the docking.

AUTODOCKProcedure:

1. Analyze  Dockings  Open…

First, you need to choose the AutoDock log file you would like to
Note: If there were a previous Docking in the
viewer, you would be asked whether you want Analyze. This command opens a file browser that lets you choose a
to add this DLG to the previous Docking file with the extension .dlg Navigate into the Results directory and
instance. This can be done when the same
AutoGrid map files, ligand, and DPF files choose imatinib_1iep_receptor.dlg. Improve the display of the
were used for both docking experiments. ligand by clicking on the circle under S&B and the diamond under
Also, WARNING messages from the docking
log can be viewed in the python shell. To do Atom in the Dashboard Widget (Appendix 2).
so, open the python shell and type

mv.docked.warnings
 Reading a docking log creates a Docking in the viewer and displays
the ligand in the lowest-energy conformation. Each conformation has a
docked energy value, a binding energy value, and per atom
electrostatic and vdw energy values. During the docking calculation,
AutoDock computes the free energy of binding and reports a detailed
energy breakdown.

ADT reports how many docked conformations were read in from the
DLG and tells you to how to visualize the docked conformations or
‘states’.

2. Analyze  Conformations  Load…

This opens ind Conformation Chooser which gives you a concise

view of the energies and clusters of the docked results.
Note: Autodock clusters by first sorting all
the docked conformations from lowest The lower panel lists the docked conformations for the ligand grouped
energy (best docking) to highest. The best according to the clustering performed at the end of the AutoDock
overall docked conformation is used as the
‘seed’ for the first cluster. Then the calculation. Double clicking on an entry in this list makes that entry
coordinates of the second best
conformation are compared with those of
the current conformation of the ligand. This results in displaying
the best to calculate the root-mean-square ligand in the viewer with new coordinates. The input conformation is
deviation between the two conformations.
If the calculated rms value is smaller than
always the first entry in this list.
the specified cutoff, which is 0.5 by
default, that conformation is added to the The upper panel displays information about the current conformation.
‘bin’ containing the best conformation. If
not, the second becomes the reference for a This includes its overall rank, for example the best result is always
second ‘bin’. Then the rms between the 1_1: lowest energy cluster_best individual in cluster. Docked Energy
third conformation and the ‘best’ is
computed . If close enough, it is added to is the sum of the intermolecular and internal energy components.
the first bin. If not it compared with the
seed of the second bin and so on…. Cluster RMS is the root mean square difference rms between this
individual and the seed for the cluster. 1_1 is the seed for the first
cluster so its Cluster RMS is 0.0. Ref RMS is the rms between the
specified reference structure. If no reference structure is specified in
the DPF, the input structure is used as the reference. freeEnergy is
the sum of the intermolecular energy plus the torsion entropy penalty
which is a constant times the number of rotatable bonds in the ligand,
kI calculated from the Docked Energy.

Double click on ind_1_1 to put the ligand in the best docked

conformation. Look at the information displayed in the top panel.
Scroll down through the list to see how many clusters were formed
with your docking results. Notice the range in energy between the
Note: lower energies are “better” ‘best’ docking and the seed of the last cluster.
and in the genetic algorithm,
“fitter.”
 Drag the lower right corner down to reveal the buttons at the bottom.
Click Dismiss.

Note: If you have read in more than one

Next we will examine the convergence of the docking result by
docking log into the current Docking or looking at its clustering. The convergence of the dockings reflects the
if the results did not include clustering,
you must Recluster… to create a thoroughness of the search. If the independent dockings produce a
clustering before you can show one. small number of conformationally-similar clusters, then the docking
searches have used a large-enough number of evaluations. If not, it is
advisable to repeat the docking calculation with an increased number
Note: if clusterings were performed using of evaluations. The number of evaluations is determined by the DPF
several different rms tolerance values, the
menu option: keyword “ga_num_evals”. In general, the more torsions a ligand has,
Analyze Clusterings Showwou the more evaluations will be needed for each docking. If the keyword
ld open a widget containing a list of the
available rms values. Be sure to click only analysis is in the DPF, AutoDock will cluster the results. By default,
once and to click delicately on this list to AutoDock clusters docked results at 2.0Å rmsd. This process
open a new interactive histogram.
(Otherwise, you may get several identical involves ordering all of the conformations by energy, from lowest to
windows.)
highest. The lowest energy conformation is used as the seed for the
first cluster. Next, the second conformation is compared to the first. If
it is within the rmsd tolerance, it is added to the first cluster. If not, it
becomes the first member of a new cluster. This process is repeated
with the rest of the docked results, grouping them into families of
similar conformations.

3. Analyze  Clusterings  Show…

Opens an interactive histogram chart labelled

‘imatinib_1iep_receptor:rms = 2.0 clustering’. This chart has bars
which represent the clusters computed at the specified rmsd. The bars
are sorted by energy of the lowest-energy conformation in that cluster
and initially are colored blue.

For example, the lowest energy conformation in the first bar is 1_1
while the lowest in second bar is 2_1. The height of the bar represents
how many conformations are in that cluster. Clicking on a bar makes
that cluster the current sequence for the ligand’s conformation player
CP, and its color changes to red. [See Appendix 3 for more details on
the CP.]

The Conformation # Info Widget shows you both refRMSD, the

rmsd between the current reference and the displayed conformation
and clRMSD, the rmsd between the displayed conformation and the
lowest energy conformation in this cluster. You can set the reference
coordinates to those of any of the docked conformations when it is the
 current conformation. When viewing clustering results, this is
especially useful because it allows you to examine the rmsd between
cluster members. To do this, choose a cluster and use the arrow key to
step forward to its lowest energy conformation, e.g. 1-1. Set the rms
reference to this conformation. Now, stepping through the cluster will
show you the rms difference between the lowest energy member of
this cluster, i.e. 1-1, and the rest of the conformations in this cluster.

You can change clusters by picking a different bar in the interactive

histogram chart. You can save this histogram as a PostScript file:
from the interactive histogram’s menu select Edit  Write to open
a file browser for you to enter a filename. Make sure to use “.ps”
extension. Select File  Exit to close.
Note: To facilitate comparing the docked
conformations, type The active site of the hiv protease has C2 symmetry. You can see
File Preferences Set
Commands to be Applied on evidence of this by comparing the lowest energy conformations in the
Objects then different clusters:
selectcolorByMolecules When this
is on, each time a new molecule is added to 1. Click on the lowest_energy bar in
the viewer (up to a current limit of 20), it is
colored differently. imatinib_1iep_receptor:rms = 2.0 clustering window to put
the ligand into conformation 1_1. Open Set Play Options
widget by clicking on the Ampersand button. Click on Build
Current
2. Build a new molecule of the conformations 2_1 by clicking on
the second_lowest_energy bar in the clustering widget
followed by clicking on Build Current
Notice how the docked conformations are symmetry related.

To recluster the results at different rms tolerances, use

Analyze  Clusterings  Recluster…
You can type in any number float values for Tolerances followed by
clicking on the OK to recluster at these rms values.

4. Evaluate the “chemical reasonableness” of the best results by

visually examining the interactions between the receptor and the best
docked conformation(s).

First, display the ligand in its lowest energy conformation using the
Conformation Player.

Next read in the receptor using:

Analyze  Macromolecule  Open…
 Finally, display a close-up of the receptor atoms interacting with the
ligand via:

Analyze  Dockings  Show Interactions

This radically changes the display, replacing the background color
with white, displaying the ligand molecular surface, spheres around
atoms in the receptor which are hydrogen-bonded or in close-contact
to atoms in the ligand plus displaying secondary structure for
sequences of 3 or more residues in the receptor which are interacting
with the ligand. The GUI for this command lets you turn on and off
different parts of this specialized display.

Examine the interactions between the ligand and nearby atoms in the
receptor:

• Is the ligand bound inside a pocket in the receptor?

• Are non-polar atoms in the ligand docked near non-polar
atoms in the receptor? Are polar atoms in the ligand
docked near polar atoms in the receptor?
Note: The interpretation of
AutoDock results is open-ended. In • If you know that a particular residue or residues in the
large part it depends on your
chemical insight and creativity.
protein interact with the ligand, is that interaction shown in
Docked poses of the ligand may the docked result?
suggest chemical modifications such
as side-group substitutions, etc…. • Do the interactions seem reasonable in the context of what
you know about your ligand-receptor from other
experimental results such as mutation studies?

Now that we have shown you the results of docking, we’re going to go
back to the very start to show you how to set up molecules for docking
and how to prepare the input files for AutoGrid and AutoDock.

Quit ADT by choosingFile  Exit and then click the OK button.

VINAProcedure:

Vina writes results as PDBQT files therefore they can be opened as

simple structure molecules. Their energy is reported in the header of
the files that can be inspected with a text editor.

1. Analyze  Dockings  Open AutoDock Vina result

Choose the Vina output file (“imatinib_out.pdbqt”), and accept the

default value “Single molecule with multiple conformations”. In this
way, the docked poses will be loaded and the keyboard arrows can be
used to walk through them.

Load the experimental structure of the ligand (“imatinib_xray.pdb”

in the “input” directory) to evaluate the quality of results.
 Exercise One: PDB Files Are Not Perfect: Editing a
PDB File

In the exercises which follow, we show you how to set up a docking

experiment. Each docking requires at least four input files:

• a PDBQT file for the ligand that encodes a torsion tree;

• a PDBQT file for the receptor;
• a grid parameter file (GPF) for the AutoGrid calculation; and
• a docking parameter file (DPF) for the AutoDock calculation.

If some residues in the receptor are to be modeled as flexible, a fifth

file will be necessary:

• a PDBQT file containing the flexible receptor residues.

Protein Data Bank (PDB) files may have a variety of problems that
need to be corrected before they can be used in AutoDock. These
potential problems include missing atoms, added waters, more than
one molecule, chain breaks, alternate locations etc.

AutoDockTools (ADT) is built on the Python Molecule Viewer

(PMV), and has an evolving set of tools designed to solve these kinds
of problems. In particular, two modules, editCommands and
repairCommands, contain many useful tools that permit you to add
or remove hydrogens, modify histidine protonation, etc. ADT cannot
do everything, though, and it is sometimes necessary to use other
software to clean up and check the quality of the structures. See the
list of resources at the AutoDock web site for a list of some of these
tools (http://autodock.scripps.edu/resources).
Note: Because of time (and sanity)
considerations, in this tutorial we only In this exercise, you will work on the macromolecule, the molecule we
demonstrate removing waters from the
receptor molecule. Nevertheless, any other want to dock to and which will be kept fixed during the dockings.
problems in the receptor and all problems in You will learn how to remove waters, how to add the hydrogens that
your ligand must be corrected also.
Remember that all hydrogens must always be
AutoDock expects, and how to save the modified result.
added prior to using ADT specific commands
to format the receptor and the ligand. Restart ADT.
 Procedure:

1. Read in the receptor molecule:

Note: Commands available via the Position the cursor over PMV Molecules in the Dashboard
Dashboard can also be invoked using the
menus at the top of the PMV GUI. Here (Appendix 2) and click with the right mouse button. This will
you could use this menu sequence to open open a file browser, showing all the files in the current
the file browser:
File->Read Molecule directory. If you are still in the Results directory, navigate up
See Appendix 2 for information about the one level by clicking on the button on the top-right of the Read
Dashboard. Molecule widget. Select 1iep_receptor.pdb and click on
Open.

This loads a Molecule named ‘1iep_receptor’ into ADT. The

bonds between bonded atoms are represented as lines while
non-bonded atoms, such as metal ions and oxygen atoms of
water molecules, are shown as small squares. The non-bonded
atoms you see here in ‘1iep_receptor’ are the oxygen atoms of
waters that were present in the crystal structure. We will
remove these waters later.

2. Color 1iep_receptor by atom type

Note: Each row in the Dashboard is linked to
a single entity. The entity is either PMV
Molecules which is the group comprised of all In the PMV Molecules row of the Dashboard, click on the
the Molecules in the Viewer, a single
Molecule, a single Chain, a single Residue or
triangle under Cl to select color the lines by Atom Type.
a single Atom. The diamonds on the right
side of the Dashboard are used to color the Now the lines representing the atoms are colored according to
displayed geometries for that row’s entity by
different coloring schemes. the chemical element, as follows:

  Carbons that are aliphatic (C) - gray,

  Carbons that are aromatic (A) - green,
 Nitrogens (N) - blue,
 Oxygens (O) - red,
 Sulfurs (S) - yellow,
 Hydrogens (H) - white.

3. Select waters and delete them

In the Dashboard click on the square under the “S”, and note
all the subsets that are available.

By selecting 'Water' all waters will be selected, and you will

see “Selected: 96 Residue(s)” with a green background in
the center of the message-bar at the bottom of the ADT
 window. Try to apply 'CPK' representation and note the the
arrangement of water clusters around the protein. Keep in mind
this for later... Right-click on “Current selection” and choose
“Delete selected atoms”. Our protein is now clean and ready to
be further processed.

5. Adding hydrogens

In the Dashboard, right-click on the receptor name and select

“Add hydrogens”.

6. Hide the protein before the next exercise by right-clicking on the

receptor name in the dashboard and select “Hide molecule”.

7. [OPTIONAL] You can save the hydrogenated receptor by selecting

it and using the menubar “File->Save->Write PDB”.
 Exercise Two: Preparing a Ligand for AutoDock.

AutoDock requires that ligands have partial atomic charges and

Note: it is assumed that all oxygen atoms can
accept hydrogen bonds and that all AutoDock atom types for each atom; it also requires a description of
hydrogens are donors. The corresponding the rotatable bonds in the ligand. AutoDock uses the idea of a tree in
default atom types are OA and HD.
Nevertheless, parameters for non-acceptor
which the rigid core of the molecule is a ‘root’, and the flexible parts
oxygens O and non-donor hydrogens H are are ‘branches’ that emanate from the root. Ligands are written in
part of default library and might be used in
some highly specialized application.
PDBQT-formatted files with special keywords recognized by
AutoDock. The keywords ROOT, ENDROOT, BRANCH, and
ENDBRANCH establish this torsion tree. The keyword TORSDOF
specifies the number of torsional degrees of freedom in the ligand. In
the AutoDock 4 force field, the TORSDOF value for a ligand is the
total number of rotatable bonds in the ligand. This number excludes
bonds in rings, bonds to leaf atoms, amide bonds, guanidinium bonds,
etc. TORSDOF is used in calculating the change in free energy caused
by the loss of torsional degrees of freedom upon binding.

For more information about the PDBQT format, see

http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-
pdbqt-file. The atom types in the PDBQT file determine atom
parameters like the van der Waals radius and the energy well depth;
these are described here http://autodock.scripps.edu/faqs-
help/faq/where-do-i-set-the-autodock-4-force-field-parameters and
here http://autodock.scripps.edu/faqs-help/faq/how-do-i-add-new-
atom-types-to-autodock-4. These parameters are used in the molecular
mechanics terms of the AutoDock scoring function: to see the form of
these equations, see: http://autodock.scripps.edu/science/equations/.

Procedure:

1. Ligand  Input  Open…

Note: We already added hydrogens to In the “Ligand File for AutoDock 4:” widget, click on the small
imatinib.mol2. You must always add
hydrogens to your ligand before you select it
bar at the right of PDBQT files: (*.pdbqt) to display a list of
to be the ligand. file type choices. Click on MOL2 files: to show all the files in
this directory and choose imatinib.mol2. Click on Open.

After the ligand is loaded in the viewer, ADT initializes it. This
process involves a number of steps:
 • ADT detects whether the ligand already has charges or not.
If not, ADT computes Gasteiger charges; remember that
for the Gasteiger calculation to work correctly, the ligand
must have all hydrogen atoms added, including both polar
and non-polar ones. If the charges are all zero, ADT will
try to add charges. It checks whether the total charge per
residue is an integer.

• ADT checks for and merges non-polar hydrogens, unless

you have set a user preference ‘adt_automergeNPHS’ not
to do so.

• ADT assigns an ‘AutoDock type’ to each atom. For peptide

Note: it is also possible to edit which planar, ligands, ADT uses a look-up dictionary for planar cyclic
cyclic carbons are assigned AutoDock_type
‘A’ but we are not going to do that in this
carbons (unless you set another user preference,
example. Also you can adjust the aromaticity ‘autotors_use ProteinAromaticList’, not to do so). For
cut-off if a ring is more warped via
Ligand  Aromatic Carbons  
other ligands, ADT determines which are planar cyclic
Aromaticity Criterion. carbons by calculating the angle between adjacent carbons
in the ring. If the angle is less than the cut-off of 7.5° (the
default value) for all the atoms in the ring, the ring carbons’
atom names will be assigned AutoDock type “A”.
Nitrogens that can accept hydrogen bonds are assigned the
AutoDock atom type ‘NA’, while those that cannot are
assigned ‘N’. In imatinib, the AutoDock type of atom N5
in the heterocycle is ‘NA’ while the other nitrogens are
Note: the PDBQT format [see below]
records the AutoDock type in the new ‘T’
assigned ‘N’. All hydrogens can donate a pair of electrons
field. Consequently, names of aromatic to a hydrogen bonds and are assigned AutoDock type
carbons do not need to start with ‘A’ as
they must for AutoDock 3.
‘HD’. Oxygens can accept hydrogen-bonds and are
assigned AutoDock type ‘OA’. Likewise, sulphur atoms
are assigned AutoDock type ‘SA’.

• ADT displays a summary for the formatted ligand that lists

what kind of charges were added, how many non-polar
hydrogens, aromatic carbons and rotatable bonds were
found, the number of torsional degrees of freedom detected
(TORSDOF) and the amount the total charge differed from
an integral value (total charge error). Click on OK to close
the summary.

2. Ligand  Torsion Tree  Detect Root…

ADT determines which atom fits its idea of the best root and
marks it with a green sphere.
 This best root is the atom in the ligand with the smallest largest
sub-tree. In the case of a tie, if either atom is in a cycle, it is
picked to be root. If neither atom is in a cycle, the first found
is picked. (If both are in a cycle, the first found is picked). As
you might imagine, this can be a slow process for large ligands.

The rigid portion of the molecule includes this root atom and
all atoms connected to it by non-rotatable bonds (which we will
examine in the next section.) You can visualize the current
root portion with Ligand  Torsion Tree 
Show Root Expansion (and hide this with Ligand 
Torsion Tree  Show/Hide Root Marker).

3. Ligand  Torsion Tree  Choose Torsions…

Opens the Torsion Count widget. The widget displays the

number of currently active bonds. Bonds that cannot be rotated
are colored red. Bonds that could be rotated but are currently
marked as inactive are colored purple. Bonds that are currently
active are colored green.

Bonds in cycles cannot be rotated. Bonds to leaf atoms cannot

be meaningfully rotated. Only single bonds can be rotated (not
double or aromatic etc). ADT determines which bonds could
be rotated (‘possibleTors’). You set which of these are to be
rotatable (‘activeTors’) by inactivating the others.

You can toggle the activity of a bond or group of bonds by

picking them in the viewer if they are displayed as lines only.
Alternatively, buttons on this widget let you toggle the activity
of a type of bonds such as ‘peptide bonds’, ‘amide bonds’,
‘bonds between selected atoms’ or ‘all rotatable bonds’. One
way to do this is to click on Make all active bonds non-
rotatable then click on Make all rotatable bonds rotatable.

Amide bonds should not be rotatable. By default, amide bonds

and aromatic amines bonds are treated as non-rotatable. You can
see that two bonds have been inactivated, the bond between atoms
N21 and C22 and that between atoms C9 and N13. Notice that the
current total number of rotatable bonds is 6. Reactivate the C9-
N13 bond and click on Done. The maximum number of rotatable
bonds allowed by AutoDock is 32, as shown on the widget: “7/32
indicates that 7 are currently active out of the maximum.
4.Ligand  Output  Save as PDBQT…

Opens a file browser allowing you to enter a name. Type in

‘imatinib.pdbqt’ and click Save.

5. Hide the root marker and the ligand before going on:

Ligand  Torsion Tree  Show/Hide Root Marker

To hide imatinib, double-click on its name in the Dashboard.

 Exercise Three: Preparing the Macromolecule.

Undisplay the ligand by double-clicking on its name and show the

receptor by clicking on the grayed receptor name (1iep_receptor).

Procedure:

1. Grid  Macromolecule  Choose…

Choose 1iep_receptor and then click Select Molecule.

Selecting the macromolecule in this way causes the following

sequence of initialization steps to be carried out automatically:

• ADT checks that the molecule has charges. If not, it

adds Gasteiger charges to each atom. Remember that all
hydrogens must be added to the macromolecule before it is
chosen. If the molecule already had charges, ADT would ask if
you want to preserve the input charges instead of adding
Gasteiger charges.

• ADT merges non-polar hydrogens and re-distributes

the atomic partial charges unless the user preferences are
Note: If ADT makes any modifications to the
molecule you opened, a file browser will open specified (adt_automergeNPHS).
for you to specify a file name. Type in a name +
“.pdbqt” and click on Save.
• ADT also determines the types of atoms in the
macromolecule. AutoDock 4 can accommodate any number of
atom types in the macromolecule.

Click OK on the WARNING dialog box. In the Modified AutoDock4

Macromolecule File: file browser, save the macromolecule in the
tutorial directory by accepting the default filename
1iep_receptor.dbqt and clicking on Save.
 Exercise Four: Preparing the Grid Parameter File.

The grid parameter file tells AutoGrid 4 which receptor to compute

Note: to specify a custom parameter library
in a grid parameter file, use the keyword the potentials around, the types of maps to compute and the location
parameter_file. See and extent of those maps. In addition it may specify a custom library
http://autodock.scripps.edu/faqs-
help/faq/where-do-i-set-the-autodock-4- of pairwise potential energy parameters. In general, one map is
force-field-parameters for more calculated for each atom type in the ligand plus an electrostatics map
information.
and a separate desolvation map.

AUTODOCKProcedure:

1. Grid  Set Map Types

The types of maps depend on the types of atoms in the ligand.

Thus one way to specify the types of maps is by choosing a
ligand. If the ligand you formatted in Exercise Six is still in the
viewer, choose Grid   Set Map Types   Choose
Ligand…, select ‘imatinib’ and click on the Select Ligand
button.

If not, use Grid   Set Map Types   Open Ligand….

Note: Alternatively, if you plan to use the Choosing the ligand opens the AutoGpf Ligand widget that
same macromolecule with a variety of
different ligands, you might choose to allows you to modify the types of maps to be calculated, and to
calculate all the maps you would eventually choose whether to model possible hydrogen bonding.
need via
Set Map Types-> Directly.
Close this widget with the Accept button.

2. Grid  Grid Box…

Opens the Grid Options Widget. First a brief tour of this

widget:

• This has menu buttons at the top: File, Center, View and
Help.

  File
 This menu lets you close the Grid Options Widget,
which also causes the grid box to disappear. You can
Close saving current values to keep your changes
or Close w/out saving to forget your changes.

  Center

This menu lets you set the center of the grid box in four
ways:   Pick an atom,   Center on ligand,
  Center on macromolecule or   On a named
atom.

  View

This menu allows you to change the visibility of the

box using Show box, and whether it is displayed as
lines or faces, using Show box as lines. This menu
also allows you to show or hide the center marker using
Show center marker and to adjust its size using
Adjust marker size.

• The “Grid Options Widget” displays the Current Total Grid

Points per map. This tells you how big each grid map will be:
(nx + 1) x (ny + 1) x (nz + 1), where nx is the number of grid
points in the x-dimension, etc.
Note: clicking with the right mouse
button on a thumbwheel widget • This has 3 thumbwheel widgets which let you change the
opens a box that allows you to type in number of points in the x, y and z dimensions. The default
the desired value directly. Like many
other entry fields in ADT, this settings are 40, 40, 40, which makes the total number of grid
updates only when you press points per map 68921 because AutoGrid always adds one in
<Enter>.
each dimension.

• You will also notice it has a thumbwheel that lets you adjust
the spacing between the grid points.

• There are also entries and thumbwheels that let you change the
location of the center of the grid.

The number of points in each dimension can be adjusted up to 126.

AutoGrid requires that the input number of grid points be an even
number. It then actually adds one point in each dimension, since
AutoGrid and AutoDock need a central grid point.

The spacing between grid points can be adjusted with another

thumbwheel. The default value is 0.375 Å between grid points, which
is about a quarter of the length of a carbon-carbon single bond. Grid
 spacing values of up to 1.0 Å can be used when a large volume is to be
investigated. If you were to need grid spacing values larger than this,
you could edit the GPF in a text editor before running AutoGrid.

For this exercise:

Adjust the number of points in to 45, 65, 55. Notice that

each map will have 170,016 points.

Type in 15.7, 53.2 and 17.5 in the x center, y center and z

center entries. This will center the grid box on kinase the active site
where the ATP binds.

Close this widget by clicking File  Close saving current.

3. Grid  Output  Save GPF…

Opens a file browser allowing the user to specify the name of

the grid parameter file. The convention is to use ‘.gpf’ as the
extension.

Write the GPF as ‘1iep_receptor.gpf’

[4. Grid  Edit GPF…

Important Note:
If you are setting up a docking If you have written a grid parameter file, it opens in an editing
using flexible residues, make window. If not, you can pick one to read in and edit via the Read
sure the specified receptor file button. If you make any changes to the content of the grid parameter
is 1iep_receptor_rigid.pdbqt. file, you can save the changes via the Write button. Edit GPF will
Grids must be calculated open the file we wrote in step 3. Either OK or Cancel close this
using a file for the molecule widget.]
without the moving residues.
VINA Procedure:

Vina grid definition requires the center coordinates x,y,z and the sizes
in Angstrom. Those values can be obtained from the Grid widget used
for the AutoGrid setup (see step 2) by changing the grid resolution to
1.00 Angstroms. Try to define a grid box the most similar to the one
used by AutoDock. For this purpose, use the same center as in the step
2, and visually inspect that the number of points 17, 24, 21 are
satisfactory.
Exercise Five: Starting AutoGrid 4

AutoGrid 4 (and AutoDock 4) must be run in the

directory where the rigid macromolecule, ligand and
parameter files are to be found.

For this reason, before running any calculation it is

important to specify the correct path where these files are.

Procedure:

1. Run  Run AutoGrid…

- In the “Working Directory” line click on the “Browse” button

to set the path where the calculation will run.

- “Program Pathname” should already contain “autogrid4”. If

not, specify the location of the executable manually by clicking
on the corresponding “Browse” button.

- On “Parameter Filename” click on the “Browse” and select

the GPF file we saved in the previous exercise
(1iep_receptor.gpf)

Here is a brief tour of this widget:

 The first two entries in the widget are used to

specify which machine to use. By default the local
machine is named in the Macro Name: entry and in
the Host name: entry. It is possible to define
macros to specify other machines with Run 
Host Preferences…
  Program Pathname: entry specifies the
location of the autogrid4 executable. If it is not in
your path, you can use Browse to locate it.

 Parameter Filename: entry specifies the GPF

file. If you have just written a GPF file, opening this
widget will automatically load the GPF filename in
the Parameter Filename: entry. If not, you can
use Browse to locate the GPF you want to use.

 Log Filename: entry specifies the log file.

Selecting a GPF creates a possible related name for
the GLG.

 Nice Level: entry used to specify a nice level

for remote jobs.

 Cmd: entry shows you the command that will

be invoked when you click on Launch.

2. Launch

Starts the AutoGrid 4 job. This opens a Process Manager that

allows you to see specifics about current AutoGrid and
AutoDock jobs.

Please note that you can easily start a job from the command line by cd
into the directory containing the input files and typing:

autogrid4 –p 1iep_receptor.gpf –l 1iep_receptor.glg &

 Exercise Six: Preparing the Docking Parameter
File.

The docking parameter file tells AutoDock which map files to use, the
ligand molecule to move, what its center and number of torsions are,
where to start the ligand, the flexible residues to move if sidechain
motion in the receptor is to be modeled, which docking algorithm to
use and how many runs to do. It usually has the file extension, “.dpf”.
Four different docking algorithms are currently available in AutoDock:
SA, the original Monte Carlo simulated annealing; GA, a traditional
Darwinian genetic algorithm; LS, local search; and GALS, which is a
hybrid genetic algorithm with local search. The GALS is also known
as a Larmarckian genetic algorithm, or LGA, because children are
allowed to inherit the local search adaptations of their parents.

Each search method has its own set of parameters, and these must be
set before running the docking experiment itself. These parameters
include what kind of random number generator to use, step sizes, etc.
The most important parameters affect how long each docking will run.
In simulated annealing, the number of temperature cycles, the number
of accepted moves and the number of rejected moves determine how
long a docking will take. In the GA and GALS, the number of energy
evaluations and the number of generations affect how long a docking
will run. ADT lets you change all of these parameters, and others not
mentioned here. See Appendix 4 Docking Parameters for more
information about individual keywords.

Procedure:
Note: If you are setting up a docking with
flexible residues , here you must select the
name of the file that contains the rigid
1. Docking  Macromolecule  Set Rigid Filename…
receptor, e.g. 1iep_receptor_rigid.pdbqt
Select 1iep_receptor.pdbqt in the file browser that opens.

Note: You can only choose a ligand if you

have previously written it to an output file
because AutoDock requires the filename of
2. Docking  Ligand  Choose…
the formatted ligand.
Choose imatinib. Click Select Ligand.
 This opens a panel that tells you the name of the current ligand,
Note: If you are modeling movement in the its atom types, its center, its number of active torsions and its
sidechains of some residues in the receptor, you number of torsional degrees of freedom. You can set a specific
must ALSO specify the name of the file
containing the formatted moving residues in the initial position of the ligand and initial relative dihedral offsets
docking parameter file. and values for its active torsions. For our exercise we will use
Docking  Macromolecule  Set
the defaults. Click Close to close this widget.
Flexible Residues Filename…

3. Docking  Search Parameters…  Genetic Algorithm…

This lets you change the genetic algorithm specific parameters.

Note: You can change the number of runs here,
too. It is a good idea to do a trial run with fewer energy evaluations.
For our exercise, we will use the short setting, i.e. 250,000
energy evaluations. This is listed as “Maximum Number of
evals”. Click Accept to continue.

4. Docking  Docking Parameters…

Here you can choose which random number generator to use,

the random number generator seeds, the energy outside the
grid, the maximum allowable initial energy, the maximum
number of retries, the step size parameters, output format
specification and whether or not to do a cluster analysis of the
results. For today, use the defaults and just click Close.

Note: ADT allows you to change the 5. Docking  Output  Lamarckian GA…
parameters for any of the four possible
docking algorithms at any time. You commit
to a specific algorithm only when you write We specify the name of the DPF we are about to write out here.
the docking parameter file. This file will contain docking parameters and instructions for
a), Lamarckian Genetic Algorithm (LGA) docking also known
as a Genetic Algorithm-Local Search (GA-LS).
Type in imatinib_1iep_receptor.dpf and click on Save.

[6. Docking  Edit DPF…

Note: If you are modelling flexibility in the
sidechains of some residues in the receptor, Use this menu option to look at the contents of the file from
the flexres keyword and a filename must
appear in the docking parameter file.
step 5. Check that the output filename, “imatinib.pdbqt”
appears after the keyword ‘move’ and that torsdof is set to “7”.
You can click either OK or Cancel to continue.
Exercise Seven:Starting AutoDock4/AutoDockVina

In general you should know that AutoDock and Vina must be run in
the directory where the macromolecule, ligand, GPF and DPF files or
config files are to be found.

AUTODOCK4Procedure:

1. Run  Run AutoDock…

- In the “Working Directory” line click on the “Browse” button

to set the path where the calculation will run.

- “Program Pathname” should already contain “autodock4”. If

not, specify the location of the executable manually by clicking
on the corresponding “Browse” button.

- On “Parameter Filename” click on the “Browse” and select

the GPF file we saved in the previous exercise
(imatinib_1iep_receptor.dpf)

Here is a brief tour of this widget:

 The first two entries in the widget are used to

specify which machine to use. By default the local
machine is named in the Macro Name: entry and in
the Host Name: entry. It is possible to define
macros to specify other machines.

 Program Pathname: entry specifies the

location of the autodock4 executable. If it is not
in your path, you can use Browse to locate it.

 Parameter Filename: entry specifies the DPF

file. If you have just written a DPF file, opening this
widget will automatically load the DPF filename in
the Parameter Filename: entry. If not, you can
use Browse to locate the DPF you want to use.
  Log Filename: entry specifies the log file.
Selecting a DPF creates a possible related name for
the DLG.

 Nice Level: entry used to specify a nice level

for remote jobs.

 Cmd: entry shows you the command that will

be invoked when you click on Launch.

2. Launch

Starts the AutoDock job. This opens a Process Manager

Widget that allows you to see specifics about current
AutoDock job. It is a limited process manager that you can use
to terminate an AutoDock process. You are asked if you really
want to kill it.

Please note that you can easily start a job from the command line by cd
into the directory containing the input files and typing:
% autodock4 –p imatinib_1iep_receptor.dpf –l
imatinib_1ieb_receptor.dlg

VINAProcedure:

1. Open a Windows terminal: Start->Run  type “cmd.exe”

cd to the Desktop directory containing the input files (HINT:

use the Tab key to complete the path):

cd C:\User\%USERNAME%\Desktop\MGL\day00\vina\input

Run Vina executable with the following syntax and

adding all the parameters in the same line:

C:\Program Files\The Scripps Research

Institute\Vina\vina.exe

--center_x 15.6 --center_y 53.2 --center_z 17.5

--size_x 17 --size_y 24 --size_z 21

--ligand imatinib.pdbqt --receptor

1iep_receptor.pdbqt
Files for Exercises:

InputFiles:
1iep_receptor.pdb
imatinib.pdb

ResultsFiles
Ligand
imatinib.pdbqt (7 torsions)
Macromolecule
1iep_receptor.pdbqt

AutoGrid
1iep_receptor.gpf
1iep_receptor.glg
1iep_receptor.*.map
1iep_receptor.maps.fld,1iep_receptor.maps.xyz
AutoDock
imatinib_1iep_receptor.dpf
imatinib_1iep_receptor.dlg

VINA
1iep_receptor.pdbqt
imatinib.pdbqt
imatinib_1iep_receptor.conf
imatinib_out*.pdbqt
 Appendix 1: PMV Basics

You might have a three-button mouse. If so, the mouse buttons can be
used alone or with a modifier key to perform different operations. To
zoom the molecule (make the molecule look bigger or smaller) in the
viewer window, press and hold down the <Shift> key and then click and
drag with the middle mouse button. To summarize what the mouse buttons
do:

Modifier Left Middle Right

On Apple Computers:.
option: Rotate None Pick Rotate
Translate left/rig
(X) and up/down
command: Translate left/right

shift+option: Scale or Zoom Scale or

Shift Select Translate in/out
shift+command: Translate in/out Zoom

Note: as you translate a molecule out in the Z You can also press the following keys in the viewer window to
dimension, it will disappear into fog which is used
for depth-cueing.
change the view of the molecule:

Key Action

R Reset view

N Normalize – scale molecule(s) so all visible molecules fit

the viewer

C Center on the center of gravity of all the molecules

Note: By default, the Viewer’s current object is D Toggle on/off Depth-cueing (blends molecule into
root so you will not see any changes here if you background farther away)
toggle between transform root and transform
current object. The DejaVu GUI lets you change
the current object.
T Toggle between transform root (i.e. scene) and transform
the Viewer’s current object.
 Appendix 2: Dashboard Widget

Select entry + Command Buttons →

Tree Widget

Note: Clicking on a shape - rectangle, circle, The Tree Widget on the left lists all molecules currently loaded in
square or diamond - under a command causes
the command linked to the shape to be applied to PMV. Click on the arrows to navigate between molecules ,
each node in the corresponding row. If the chains , residues and atoms . Clicking on a shape in
shape is off (colored white), the command will
be applied to nodes and the shape will be colored one of the columns in the right section executes the PMV
red. If the shape is on (colored red), clicking on command corresponding to the label at the top of the column on
the command button will undo the command and
the shape will be colored white. Circles are used the group of nodes corresponding to the row. There 16 different
for display commands, squares for label commands that can be executed this way - gray rectangle
commands and diamonds for color commands.
Coloring can be replaced by a different coloring (Show/Hide), select/unselect (Sel.), display lines (Lines), display
scheme but cannot be undone. The gray CPK (CPK), display sticks and balls (S&B), display secondary
rectangle is used for show/hide and the white
rectangle for select. structure (Rib.), display molecular surface (MS), display labels
(Lab.), color by atom type (Atom), color by molecule (Mol), color
by chain (Chain), color by residue according Rasmol (RAS), color
by residue according Shapely (SHA), color according to David
Goodsell colors (DG), color by secondary structure element type
(Sec.Str.) and color by instance (Inst).

To help users see the connection between molecular fragments and

PMV commands, a crosshair is drawn when cursor is inside the
Dashboard widget.

Right-clicking on a shape displays an input parameter panel for the

command and allows the user to customize specific input
parameters for the command.

Note: A selection in the Tree is used to build a The Sel: entry in the top left corner of the Dashboard can be used
group of nodes to be the target for commands
linked to shapes. It is not the same as the current to select entries in the Tree using a Pmv compound selector. Nodes
selection in the Viewer. It can be selected using matching the specified string will be selected. Selected nodes are
the appropriate rectangles….
outlined with a yellow selection box. When a shape is clicked for
a selected node, the corresponding command is applied to all
currently selected nodes. Hovering over this entry shows samples
of the required syntax.
The option menu on the top allows the user to specify whether
commands should be applied to the backbone atoms only (BB), the
side chain atoms only (SC), the sidechain atoms and CA atoms
(SC+CA) or the full molecular fragment (ALL). This setting can
be overridden for each column (CMD).

Click on the gray rectangle under Show/Hide. Notice that the

molecule in the viewer disappears. Click on the same rectangle
again to redisplay it. Click on the rectangle under the Sel level to
select or deselect all. Experiment by clicking on each of the other
buttons. These are short cuts to a basic set of commands for
displaying and coloring various molecular representations.
Appendix 3: Conformation Player

• Type-in entry at center for random access to any

conformation by its id. Valid ids depend on which menubutton
was last used to start the player.

• Click on black arrow buttons next to entry to change to next

or previous conformation in current list.

• White arrow buttons start play according to current play

mode parameters (see below). Clicking on an active white arrow
button stops play. [While a play button is active, its icon is
changed to double vertical bars.]

• Double black arrow buttons start play as fast as possible in

the specified direction.

• Double black arrow plus line buttons advance to

beginning or end of conformation list.

• Ampersand button opens the Set Play Options widget (see

next).

• Quatrefoil button closes the player.

Next, a tour of the Set Play Options widget and its buttons:
 • Show Info opens and closes a separate panel Conformation # Info
Note: building hydrogen bonds
requires that the receptor molecule be which displays additional information about current conformation
present in the viewer and that you (see following).
have either chosen it using:

Analyze Macromolecule
• Build H-bonds turns on and off building and displaying hydrogen
Choose or read it in specifically bonds between the macromolecule and the ligand in its current
using conformation.
Analyze Macromolecule
Open…
• Color by allows you to choose how to color the ligand from a list
of available coloring schemes.

• Show Conf List opens and closes a separate Choose

Conformations widget showing current idlist (see below).

• Make clust RMS ref sets the reference coordinates for RMS to
those of the current conformation. [This RMS value is shown in Info
panel as clRMS]

• Choose mol for RMS ref lets you select a different molecule
from list of those in Viewer to use as reference for a new RMS
computation.

• Play Mode opens a separate Play Mode widget (see next).

• Play Parameters exposes controls for setting parameters

governing how the conformations are played:

Note: To set the value of a thumbwheel

click on it with the left mouse button and
hold the mouse button down while you
drag the mouse to the right to increase the
value or to the left to decrease the value.
Alternatively, you can right-click on a
thumbwheel to open a separate widget
which lets you type in a new value.

Note: the input conformation of the ligand

is always inserted at the list of Four thumbwheel widgets are used to set Play Parameters.
conformations . It is always conformation
0. • frame rate: set the relative speed of the player
[absolute rate is cpu dependent]
 • start frame: index into current conformation list.
Note the input conformation is always inserted at
index 0 in sequence list.
• end frame: index into current conformation list.
• step size: determines next conformation in list. For
example, step size 1 plays every available
conformation whereas step size 2 every other…

Clicking on Play Parameters hides the thumbwheels.

• Build Current adds a new molecule to the viewer with current

conformation’s coordinates providing that a molecule hasn’t already
been built with this conformation’s id.

• Build All builds a new molecule for each conformation in the

current sequence of conformations bound to the player.

• Write Current lets you choose a filename for writing a formatted

file using the current coordinates.

• Write All writes a formatted file for each set of coordinates in the
current sequence. This uses default filenames based on the id of
each Conformation.

• Close button closes Set Play Options widget.

Next, the Play Mode widget and its buttons:

These 4 radiobuttons are used to set the current play mode. [Note that at any
time, the current endFrame and the current startFrame depend on the
direction of play.]

• once and stop plays from the current conformation in the current
direction up to and including the endFrame.

• continuously in 1 direction plays in the current direction up to

and including the endFrame and then restarts with startFrame , again
and again….
 • once in 2 directions plays from the current conformation in the
current direction up to and including the endFrame and then plays
back to startFrame and stops.

• continuously in 2 directions plays from current conformation

in current direction up to endFrame then back to the beginning then
back to the end, again and again….
•

The Choose Conformation widget:

Choose Conformation widget has list of ids for each conformation in the
current sequence list. Double clicking on an entry in this list updates the
ligand to the corresponding conformation. This widget is closed by clicking
on the checkbutton Show Conf List in Set Play Options widget.

Conformation # Info widget shows information about a specific

conformation from a docking experiment.

• binding energy is the sum of the intermolecular energy and the

torsional free-energy penalty.

• docking energy is the sum of the intermolecular energy and the

ligand’s internal energy.
• inhib_constant is calculated in AutoDock as follows:

Ki=exp((deltaG*1000.)/(Rcal*TK)
where deltaG is docking energy, Rcal is 1.98719 and TK is 298.15

• refRMS is rms difference between current conformation coordinates

and current reference structure. By default the input ligand is used as
the reference.

• clRMS is rms difference between current conformation and the

lowest energy conformation in its cluster.

• torsional_energy is the number of active torsions * .3113

[.3113 is AutoDock 3 forcefield torsional free energy parameter]

• rseed1 and rseed2 are the specific random number seeds used for
current conformation’s docking run.
Appendix 4: Docking Parameters

Parameterscommonto SA, GA, GALS:

‘parameter_file’: optional file containing a user-defined library of

customized parameters.

'seed': The number of arguments following this keyword

determines which random number generator is to be used. One
argument causes AutoDock to use the system’s implementation of the
random number generator and a corresponding system seed call. One
argument is required for the simulated annealing algorithm. Two
arguments tells AutoDock to use the platform-independent library for
random number generation. Two arguments are required for the
genetic algorithm. The arguments themselves can be any combination
of explicit long integers, the key word ‘time’ or the keyword ‘pid’.
‘time’ is the number of seconds since the epoch, referenced to
00:00:00CUT 1 Jan 1970. ‘pid’ gives the UNIX process ID of the
currently executing AutoDock process.

'ligand_types': all AutoDock 4 atom types present in ligand. If

flexible residues are to be docked, their atom types must be included.

'fld': grid data field file created by AutoGrid and readable by AVS.

'map': filename for the first AutoGrid affinity grid map of the 1st
atom type. Repeated for all atom types specified in ‘ligand_types’.

'elecmap': filename for the required electrostatics map.

'desolvmap': filename for the required desolvation map.

'flexres': optional filename for the flexible residues to be docked.

'unbound <value>': optional reference energy ‘value’ for the

unbound extended state of the ligand to be docked. If many dockings
are to be done with the same input ligand, it is not necessary to
compute the unbound extended energy for each. Instead, it could be
included in subsequent docking parameter files using this keyword.
 ‘unbound_intnbp_coeffs’: optional internal pairwise non-bonded
energy parameters for the unbound energy calculation for the flexible
ligand: equilibrium distance and well depth followed by integer
exponents n and m.

‘include_1_4_interactions’: optional flag to include the pairwise-

energy for atoms separated by three bonds in the internal energy
calculation. By default the interaction energy of atoms separated by 3
bonds is not included.

‘epdb filename’: optional calculate the energy of the molecule in

filename in the context of the specified maps. Previously this feature
was only accessible via the command-mode of AutoDock 3. The
command-mode is no longer supported in AutoDock 4.

'about': x y z center of ligand about which rotations will be made.

Coordinate frame of reference inside AutoDock. That is, internally the
ligand’s coordinates become centered at the origin. If flexible residues
are to be included in the docking, their atom positions are not included
in determining the ‘about’ value: it remains the center of the ligand
atoms only.

'reorient': apply an initial reorientation to the ligand either

random, standard which moves the ligand such that the first three
atoms lie parallel to the xy-plane and the first two atoms lie parallel to
the x-axis or <axis-x> <axis-y><axis-z> to apply a specific rotation to
the input ligand.

'tran0': initial coordinates for the center of the ligand or random.

Each new run starts the ligand from this location. Please note: the user
should enscure that the ligand, when translated to these coordinates
still fits inside the volume of the grid maps. If there are some atoms
which do lie outside this volume, AutoDock will automatically move
the ligand until the ligand is completely inside the box.

'quat0': deprecated now use either quaternion0 or axisangle0.

‘quaternion0: initial quaternion Qx, Qy, Qz, Qw or random.

'axisangle0: initial axis and angle for rotation Qx, Qy, Qz, Qang or
random.

'ndihe': deprecated AutoDock 4 determines the number of rotatable

bonds from the PDBQT file of the ligand and flexible residues file (if
there is one).
 'dihe0': optional initial relative dihedral angles or random. There
must be a value specified for each rotatable bond in the ligand (and
optional flexres file) if the user decides to explicitly set the initial
relative dihedrals.

'tstep': if one argument, the maximum translation jump per step. If

single argument and less than one, the reduction factor is multiplied
with the tstep at the end of each cycle to get next value. Alternatively,
if there are two arguments, the user specifies the value for the first and
last cycle and AutoDock calculates the reduction factor that satisfies
these constraints. Default is 2.0 Angstrom

'qstep': maximum orientation step size for the angular component

w of quaternion. Default is 50.0 degrees.

'dstep': maximum dihedral step size. Default is 50.0 degrees.

'torsdof': number of the torsional degrees of freedom for the

estimation of the change of free energy upon binding. For AutoDock 4
this is,the number of possible rotatable bonds in the ligand. This
differs from torsdof for AutoDock 3 which excluded any torsions that
only rotated hydrogens: eg hydroxyls, amines.

'intelec': always calculate internal ligand electrostatic energies for

AutoDock 4.

'outlev': diagnostic output level. For simulated annealing 0= no

output, 1=minimal output, 2 = full state output at end of each cycle,
3=detailed output for each step. For GA and GA-LS: 0=minimal
output, 1= write minimum, mean and maximum of each state variable
at the end of every generation. Use outlev 1 for SA and outlev 0 for
GA and GA-LS.

'rmstol': the rms deviation tolerance for cluster analysis, carried out
after multiple docking runs. If two conformations have an rms less
than this tolerance, they will be placed in the same cluster. The
structures are ranked by energy, as are the clusters.

'rmsatoms': optional the base for cluster analysis by default is ‘all’

atoms. In a docking involving flexible residues, it is possible to cluster
using only the ligand atoms. To do so, include this keyword with the
value ‘ligand_only’

'rmsref': optional the root mean square deviation of the docked

conformations calculated with respect to the coordinates in the
PDBQT file or PDB file specified here. Particularly useful for
comparing a docked result to a known crystal structure.

'extnrg': optional external grid energy assigned to any atoms that

stray outside the volume of the grid during a docking. Default is 1000.
kcal/mole.

‘compute_unbound_extended’: use a specialized force field with

no internal electrostatics to drive the ligand into an extended
conformation and compute the energy of this extended state. This is
used in the AutoDock 4 force field as the unbound energy of the input
ligand. If the unbound extended energy of the ligand is specified using
the keyword unbound, compute_unbound_extended becomes
optional.

'analysis': perform a cluster analysis on results of a docking and

output results to the log file. The docked conformations are sorted in
order of increasing energy, then compared by root mean square
deviation. If the docked result is within the ‘rmstol’ threshold, it is
placed into the same cluster.

SimulatedAnnealingSpecificParameters:

'rt0': initial annealing temperature-actually absolute temperature

multiplied by the gas constant. Default is 500. cal/mole.

'e0max': two floats-used only in SA. Keyword stipulates that the

ligand’s initial state cannot have an energy greater than the first value,
nor can there be more than the second value’s number of retries.
Default is 0, 10000.

'linear_schedule': instructs AutoDock to use a linear temperature

reduction schedule during Monte Carlo simulated annealing. Unless
given, a geometric reduction schedule is used according to rtrf
described below. Default is to use linear_schedule.

'rtrf': annealing temperature reduction factor. At the end of each

cycle the annealing temperature is multiplied by this factor to give that
of the next cycle. Must be positive and less than one. Default is 0.95

'trnrf': per cycle reduction factor for translations. Default is 1.0.

'quarf': per cycle reduction factor for quaternions. Default is 1.0.

 'dihrf': per cycle reduction factor for dihedrals. Default is 1.0

'runs': number of automated docking runs to carry out. Default is

10.

'cycles': number of temperature reduction cycles. Default is 50.

'accs': Maximum number of accepted steps per cycle. Default is

100.

'rejs': Maximum number of rejected steps per cycle. Default is 100.

'select': State selection flag. ‘m’ minimum state is selected or ‘l’ last
state. Default is m.

'simanneal': instructs AutoDock to do specified number of docking

runs using the simulated annealing SA search engine.

GeneticAlgorithmSpecificParameters:

'ga_pop_size': number of individuals in the population. Each

individual is a coupling of a genotype and its associated phenotype.
Typical values range from 50 to 200. Default is 50.

‘output_pop_file’ optional filename to write populations.

'ga_num_evals':Maximum number of energy evaluations that a GA

run should make. Default is 250000.

'ga_num_generations': Maximum number of generations that a

GA or LGA run should last. Default is 27000.

'ga_elitism': Number of top individuals that are guaranteed to

survive into the next generation. Default is 1.

'ga_mutation_rate': The probability that a particular gene is

mutated. Default is 0.02

'ga_crossover_rate': Crossover rate is the expected number of pairs

in the population that will exchange genetic material. Setting this
value to 0 turns the GA into the evolutionary programming method
(EP) but that requires a concomitant increase in the ga_mutation_rate
in order to be effective. Default is 0.80.

'ga_window_size': Number of preceding generations to take into

consideration when deciding the threshold for the worst individual in
the current population. Default is 10.

'ga_cauchy_alpha': Alpha parameter in a Cauchy distribution

which corresponds roughly to the mean of the distribution. Default is
0.

'ga_cauchy_beta': Beta parameter in a Cauchy distribution which

corresponds roughly to something like the variance of the distribution.
However, the Cauchy distribution doesn’t have finite variance.
Default is 1.

'set_ga': sets the global optimizer to be a genetic algorithm.

PLEASE note all ga_ parameters must be specified before this line in
order to be used in the docking.

'do_global_only': instructs AutoDock to carry out docking using

only a global search. Local search parameters in the DPF are ignored
when this is present.

LocalSearchSpecificParameters:

'sw_max_its': Maximum number of iterations that the local search

procedure applies to the phenotype of any given individual. Default is
50.

'sw_max_succ': Number of successes in a row before a change is

made to the rho parameter in Solis & Wets algorithm. Default is 4.

'sw_max_fail': Number of failures in a row before Solis & Wets

algorithms adjust rho. Default is 4.

'sw_rho': Parameter defining the initial variance and specifying the

size of the local space to sample. Default is 1.0.

'sw_lb_rho': Lower bound on rho, the variance for making changes

to genes. Rho can never be modified to a value smaller than
sw_lb_rho. Default is 0.01.
 'ls_search_freq': The probability of any particular phenotype being
subjected to local search. Default is 0.06.

'set_psw1': Instructs AutoDock to use the pseudo-Solis and Wets

local searcher. This method maintains the relative proportions of
variances for the translations in Angstrom and the rotations in radians.
These are typically 0.2 Angstrom and 0.087 radians to start with so the
variance for translations will always be 2.3 times larger than that for
the rotations (i.e. the orientation and torsions).

'do_local_only': Instructs AutoDock to carry out only the local

search of a global-local search. The genetic algorithm parameters are
ignored, except for the population size. This is an ideal way of
carrying out a minimization using the same force field as is used
during the dockings. The ga_run keyword should not be given. The
integer following the keyword determines how many dockings will be
performed. Default is 50.

GALS parameters include all Genetic Algorithm and Local Search

parameters listed above except do_global_only and do_local_only.

ClusteringKeywords:

'cluster': keyword specific to reclustering jobs. Parameter which

follows is filename for concatenated docking logs. Script ‘recluster.py’
produces this kind of file.

'rmstol': root mean square tolerance for reclustering.

'ligand_types': types of atoms present in ligand

'write_all': option causes printed output of all docked structures in

each cluster. Default is to write the first docked structure in each
cluster only. (The first docked structure has the lowest energy of all
the docked structures in the cluster.)