Difference between revisions of "AutoDock4 Pose Reproduction Tutorial"
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The purpose of this tutorial is to provide members of the Rizzo lab a way to benchmark the AutoDock4 software to compare the Pose Reproduction success rates against the DOCK6 software. | The purpose of this tutorial is to provide members of the Rizzo lab a way to benchmark the AutoDock4 software to compare the Pose Reproduction success rates against the DOCK6 software. | ||
(Note: The program version used for this experiment was AutoDock4.2.6 and DOCK6.9 | (Note: The program version used for this experiment was AutoDock4.2.6 and DOCK6.9 | ||
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| + | ==I. Introduction== | ||
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==II.Prepping Directories== | ==II.Prepping Directories== | ||
Revision as of 13:54, 17 July 2020
The purpose of this tutorial is to provide members of the Rizzo lab a way to benchmark the AutoDock4 software to compare the Pose Reproduction success rates against the DOCK6 software. (Note: The program version used for this experiment was AutoDock4.2.6 and DOCK6.9
I. Introduction
II.Prepping Directories
First step is prepare a file with a list of systems within it. For this docking experiment this file was called clean.systems.all
121P 181L 182L 183L 184L etc
Second step run the run.000.AutoDock.source.sh script to prepare a directory for each system in the file. The 1st arguement is the list of systems file made in the previous step. The 2nd Arguement is the new directory that will be made where all the AutoDock4 experiments will be performed
bash ./run.000.AutoDock.source.sh ../clean.systems.all AutoDock4_Tutorial
The directory where all the directories will be formed is
AutoDock4_Tutorial/
Each System will have it's own directory in this file
AutoDock4_Tutorial/121P/ AutoDock4_Tutorial/181L/ AutoDock4_Tutorial/182L/ etc
