From 8fa0d4cc58b844d84f7b1bf6f269162b645a2f0d Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Mon, 23 Nov 2020 19:39:48 +0530 Subject: Publish deploy 2020-11-23 19:39 --- .../index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (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 081e1f6..87ff8e2 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 @@ -1,4 +1,4 @@ -Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan
Navan Chauhan
2 minute readCreated on June 1, 2020Last modified on September 15, 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 -:"$(pbpaste)" --gen3d -opdbqt -Otest.pdbqt && vina --receptor lu.pdbqt --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3  --ligand test.pdbqt
+Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan
Navan Chauhan
2 minute readCreated on June 1, 2020Last modified on September 15, 2020
Workflow for Lightning Fast Molecular Docking Part One
My Setup
  • macOS Catalina ( RIP 32bit app)
  • PyMOL
  • AutoDock Vina
  • Open Babel
One Command Docking
obabel -:"$(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'
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