From 3ec7d22d1ca0c5a5bbd54a735f917aebab633928 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Mon, 1 Jun 2020 12:33:18 +0530 Subject: Publish deploy 2020-06-01 12:33 --- feed.rss | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'feed.rss') diff --git a/feed.rss b/feed.rss index 3f63420..306d50a 100644 --- a/feed.rss +++ b/feed.rss @@ -1,4 +1,4 @@ -Navan ChauhanWelcome to my personal fragment of the internet. Majority of the posts should be complete.https://navanchauhan.github.io/enMon, 1 Jun 2020 12:27:03 +0530Mon, 1 Jun 2020 12:27:03 +0530250https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOLWorkflow for Lightning Fast Molecular Docking Part OneThis is my workflow for lightning fast molecular docking.https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOLMon, 1 Jun 2020 13:10:00 +0530Workflow for Lightning Fast Molecular Docking Part One

My Setup

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

One Command Docking

obabel -:"$(pbpaste)" --gen3d -opdbqt -Otest.pdbqt && vina --receptor lu.pdbqt --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3  --ligand test.pdbqt
+Navan ChauhanWelcome to my personal fragment of the internet. Majority of the posts should be complete.https://navanchauhan.github.io/enMon, 1 Jun 2020 12:33:11 +0530Mon, 1 Jun 2020 12:33:11 +0530250https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOLWorkflow for Lightning Fast Molecular Docking Part OneThis is my workflow for lightning fast molecular docking.https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOLMon, 1 Jun 2020 13:10:00 +0530Workflow for Lightning Fast Molecular Docking Part One
My Setup
  • macOS Catalina ( RIP 32bit app)
  • PyMOL
  • AutoDock Vina
  • Open Babel
One Command Docking
obabel -:"$(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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