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finish editing basic docking
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rwxayheee committed Oct 24, 2024
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147 changes: 63 additions & 84 deletions docs/source/docking_basic.rst
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Expand Up @@ -31,7 +31,8 @@ The input and expected output files can be found here on `GitHub <https://github

During this step, we will create a PDBQT file of our receptor containing only the polar hydrogen atoms as well as partial charges. For this step, we will use the ``mk_prepare_receptor.py`` command-line script:

::
.. code-block:: bash
$ mk_prepare_receptor.py -i 1iep_receptorH.pdb -o 1iep_receptor -p -v \
--box_size 20 20 20 --box_center 15.190 53.903 16.917
Expand Down Expand Up @@ -69,41 +70,18 @@ Other options are available for ``mk_prepare_ligand.py`` by typing ``mk_prepare_

To use the AutoDock FF in docking, we need an additional input file, which is the grid parameter file (GPF) for AutoGrid4, to create an affinity map file for each atom types. The GPF file specifies an AutoGrid4 calculation, including the size and location of the grid, the atom types that will be used, the coordinate file for the rigid receptor, and other parameters for calculation of the grids.

To prepare the gpf file for AutoGrid4, you can rerun ``mk_prepare_receptor.py`` command line tool.
To prepare the gpf file for AutoGrid4, you can run (or rerun) ``mk_prepare_receptor.py`` with the additional option, ``-g`` that will enable the writing of the GPF file.

.. code-block:: bash
$ pythonsh <script_directory>/prepare_gpf.py -l 1iep_ligand.pdbqt -r 1iep_receptor.pdbqt -y
The option ``-y`` specifies that we want to center automatically the grid around the ligand. For more information about ``prepare_gpf.py``, type ``pythonsh prepare_gpf.py -h``. At the end you should obtain the following GPF file ``1iep_receptor.gpf`` containing those lines:


.. code-block:: console
:caption: Content of the grid parameter file (**1iep_receptor.gpf**) for the receptor c-Abl (**1iep_receptor.pdbqt**)
npts 54 54 54 # num.grid points in xyz
gridfld 1iep_receptor.maps.fld # grid_data_file
spacing 0.375 # spacing(A)
receptor_types A C OA N SA HD # receptor atom types
ligand_types A C NA OA N HD # ligand atom types
receptor 1iep_receptor.pdbqt # macromolecule
gridcenter 15.190 53.903 16.917 # xyz-coordinates or auto
smooth 0.5 # store minimum energy w/in rad(A)
map 1iep_receptor.A.map # atom-specific affinity map
map 1iep_receptor.C.map # atom-specific affinity map
map 1iep_receptor.NA.map # atom-specific affinity map
map 1iep_receptor.OA.map # atom-specific affinity map
map 1iep_receptor.N.map # atom-specific affinity map
map 1iep_receptor.HD.map # atom-specific affinity map
elecmap 1iep_receptor.e.map # electrostatic potential map
dsolvmap 1iep_receptor.d.map # desolvation potential map
dielectric -0.1465 # <0, AD4 distance-dep.diel;>0, constant
$ mk_prepare_receptor.py -i 1iep_receptorH.pdb -o 1iep_receptor -p -v -g \
--box_size 20 20 20 --box_center 15.190 53.903 16.917
After creating the GPF file, and now we can use the ``autogrid4`` command to generate the different map files that will be used for the molecular docking:

.. code-block:: bash
$ autogrid4 -p 1iep.gpf -l 1iep.glg
$ autogrid4 -p 1iep_receptor.gpf -l 1iep_receptor.glg
From this command you should have generated the following files:

Expand Down Expand Up @@ -134,10 +112,10 @@ Running AutoDock Vina will write a PDBQT file called ``1iep_ligand_ad4_out.pdbqt
4.b. Using Vina forcefield
__________________________

Contrary to AutoDock4, you don't need to precalculate the affinity grid maps with ``autogrid4`` when using the Vina forcefield. AutoDock Vina computes those maps internally before the docking. However, you still need to specify the center and dimensions (in Angstrom) of the grid space, as well as the receptor. Here, instead of specifying each parameters for the grid box using the arguments ``--center_x, --center_y, --center_z`` and ``--size_x, --size_y, --size_z``, we will store all those informations in a text file ``1iep_receptor_vina_box.txt``.
Contrary to AutoDock4, you don't need to precalculate the affinity grid maps with ``autogrid4`` when using the Vina forcefield. AutoDock Vina computes those maps internally before the docking. If you did not make the box dimension file when preparing receptor in the previous step, you could specify the center and dimensions (in Angstrom) of the grid box in a new TXT file:

.. code-block:: console
:caption: Content of the config file (**1iep_receptor_vina_box.txt**) for AutoDock Vina
:caption: Content of the config file (**1iep_receptor.box.txt**) for AutoDock Vina
center_x = 15.190
center_y = 53.903
Expand All @@ -149,7 +127,7 @@ Contrary to AutoDock4, you don't need to precalculate the affinity grid maps wit
.. code-block:: bash
$ vina --receptor 1iep_receptor.pdbqt --ligand 1iep_ligand.pdbqt \
--config 1iep_receptor_vina_box.txt \
--config 1iep_receptor.box.txt \
--exhaustiveness=32 --out 1iep_ligand_vina_out.pdbqt
.. tip::
Expand All @@ -174,30 +152,31 @@ The predicted free energy of binding should be about ``-14 kcal/mol`` for poses

.. code-block:: console
Scoring function : ad4
Ligand: 1iep_ligand.pdbqt
Exhaustiveness: 32
CPU: 0
Verbosity: 1
Reading AD4.2 maps ... done.
Performing docking (random seed: -556654859) ...
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -14.62 0 0
2 -13.13 1.051 1.529
3 -12.26 1.442 2.158
4 -11.91 3.646 11.5
5 -11.89 3.859 11.99
6 -11.47 1.978 13.56
7 -11.33 1.727 2.585
8 -10.85 3.619 5.759
9 -10.23 7.057 12.7
Scoring function : ad4
Ligand: 1iep_ligand.pdbqt
Exhaustiveness: 32
CPU: 0
Verbosity: 1
Reading AD4.2 maps ... done.
Performing docking (random seed: 1045208650) ...
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -14.72 0 0
2 -14.63 0.862 1.051
3 -13.12 1.152 1.877
4 -11.7 4.989 11.38
5 -11.44 3.619 11.51
6 -11.39 1.36 2.222
7 -11.21 3.773 12.06
8 -10.71 2.043 13.49
9 -10.41 1.748 2.955
5.b. Using Vina forcefield
__________________________
Expand All @@ -206,31 +185,31 @@ Using the vina forcefield, you should obtain a similar output from Vina with the

.. code-block:: console
Scoring function : vina
Rigid receptor: 1iep_receptor.pdbqt
Ligand: 1iep_ligand.pdbqt
Center: X 15.19 Y 53.903 Z 16.917
Size: X 20 Y 20 Z 20
Grid space: 0.375
Exhaustiveness: 32
CPU: 0
Verbosity: 1
Computing Vina grid ... done.
Performing docking (random seed: -131415392) ...
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -12.92 0 0
2 -10.97 3.012 12.42
3 -10.79 3.713 12.19
4 -10.69 3.913 12.36
5 -10.32 2.538 12.64
6 -9.464 2.916 12.53
7 -9.204 1.35 2.025
8 -9.137 1.596 2.674
9 -8.637 3.969 12.69
Scoring function : vina
Rigid receptor: 1iep_receptor.pdbqt
Ligand: 1iep_ligand.pdbqt
Grid center: X 15.19 Y 53.903 Z 16.917
Grid size : X 20 Y 20 Z 20
Grid space : 0.375
Exhaustiveness: 32
CPU: 0
Verbosity: 1
Computing Vina grid ... done.
Performing docking (random seed: -1622165383) ...
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -13.23 0 0
2 -11.29 0.9857 1.681
3 -11.28 3.044 12.41
4 -11.15 3.813 12.24
5 -9.746 3.313 12.36
6 -9.132 1.736 13.47
7 -9.079 2.559 12.78
8 -8.931 3.951 12.69
9 -8.762 3.541 12.21
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