From 2f41128c0e74d5189f4e1bf86f5d3658acc1d22a Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Tue, 2 Jun 2020 23:25:49 +0530 Subject: Publish deploy 2020-06-02 23:25 --- .../index.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL') diff --git a/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html b/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html index f7ac7fa..0da2ef5 100644 --- a/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html +++ b/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html @@ -1,8 +1,8 @@ -Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan
Navan Chauhan
2 minute readCreated on June 1, 2020

Workflow for Lightning Fast Molecular Docking Part One

My Setup

  • macOS Catalina ( RIP 32bit app)
  • PyMOL
  • AutoDock Vina
  • Open Babel

One Command Docking

obabel -:"$(pbpaste)" --gen3d -opdbqt -Otest.pdbqt && vina --receptor lu.pdbqt --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3  --ligand test.pdbqt
+Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan
Navan Chauhan
2 minute readCreated on June 1, 2020Last modified on June 2, 2020
Workflow for Lightning Fast Molecular Docking Part One
My Setup
  • macOS Catalina ( RIP 32bit app)
  • PyMOL
  • AutoDock Vina
  • Open Babel
One Command Docking
obabel -:"$(pbpaste)" --gen3d -opdbqt -Otest.pdbqt && vina --receptor lu.pdbqt --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3  --ligand test.pdbqt
 
To run this command you simple copy the SMILES structure of the ligand you want an it automatically takes it from your clipboard, generates the 3D structure in the AutoDock PDBQT format using Open Babel and then docks it with your receptor using AutoDock Vina, all with just one command.
Let me break down the commands
obabel -:"$(pbpaste)" --gen3d -opdbqt -Otest.pdbqt
 
pbpaste and pbcopy are macOS commands for pasting and copying from and to the clipboard. Linux users may install the xclip and xsel packages from their respective package managers and then insert these aliases into their bash_profile, zshrc e.t.c
alias pbcopy='xclip -selection clipboard'
 alias pbpaste='xclip -selection clipboard -o'
 
$(pbpaste)
 
This is used in bash to evaluate the results of a command. In this scenario we are using it to get the contents of the clipboard.
The rest of the command is a normal Open Babel command to generate a 3D structure in PDBQT format and then save it as test.pdbqt
&&
 
This tells the termianl to only run the next part if the previous command runs succesfuly without any errors.
vina --receptor lu.pdbqt --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3  --ligand test.pdbqt
-
This is just the docking command for AutoDock Vina. In the next part I will tell how to use PyMOL and a plugin to directly generate the coordinates in Vina format  --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3 without needing to type them manually.
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This is just the docking command for AutoDock Vina. In the next part I will tell how to use PyMOL and a plugin to directly generate the coordinates in Vina format --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3 without needing to type them manually.

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