Workflow for Lightning Fast Molecular Docking Part One

My Setup

macOS Catalina ( RIP 32bit app)
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

-- cgit v1.2.3 From 9e620084e57378952c1a7f8e0a772ebebd18932b Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Wed, 27 Mar 2024 20:35:09 -0600 Subject: quick fix --- ...eding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html') diff --git a/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html b/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html index cc8baf5..8126a04 100644 --- a/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html +++ b/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html @@ -6,13 +6,13 @@ - id="workflow-for-lightning-fast-molecular-docking-part-one">Workflow for Lightning Fast Molecular Docking Part One + Workflow for Lightning Fast Molecular Docking Part One - Workflow for Lightning Fast Molecular Docking Part One" /> - Workflow for Lightning Fast Molecular Docking Part One" /> + + -- cgit v1.2.3 From 01ff93c9c16867216f2d249664803860e1d6d5eb Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Wed, 27 Mar 2024 22:49:40 -0600 Subject: generate new theme --- ...r-Docking-Workflow-AutoDock-Vina-and-PyMOL.html | 55 +++++++++++++++------- 1 file changed, 37 insertions(+), 18 deletions(-) (limited to 'docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html') diff --git a/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html b/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html index 8126a04..b396ad6 100644 --- a/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html +++ b/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html @@ -2,14 +2,26 @@ - + + + + + Workflow for Lightning Fast Molecular Docking Part One + + + + + + + - Workflow for Lightning Fast Molecular Docking Part One - @@ -29,21 +41,27 @@ - - - + + +

- +

Workflow for Lightning Fast Molecular Docking Part One

My Setup

@@ -90,14 +108,15 @@ alias pbpaste='xclip -selection clipboard -o'

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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-- cgit v1.2.3 From de19543d7fb44d343b052dc9b34ede78620c4a46 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Wed, 27 Mar 2024 23:36:55 -0600 Subject: Generate --- ...lecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) (limited to 'docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html') diff --git a/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html b/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html index b396ad6..1bde992 100644 --- a/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html +++ b/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html @@ -46,7 +46,7 @@ + +

-- cgit v1.2.3 From a982ceab0b45609991179b3020a00260eed6f798 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Wed, 27 Mar 2024 23:45:59 -0600 Subject: css --- ...1-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html | 1 + 1 file changed, 1 insertion(+) (limited to 'docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html') diff --git a/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html b/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html index 1bde992..32abeda 100644 --- a/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html +++ b/docs/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html @@ -5,6 +5,7 @@ + Workflow for Lightning Fast Molecular Docking Part One -- cgit v1.2.3