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 --- .../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/index.html') 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 aa9ff67..f7ac7fa 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 @@ -5,4 +5,4 @@ 
$(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.

Tagged with:
\ No newline at end of file -- cgit v1.2.3