Difference between revisions of "2023 AMBER tutorial 3 with PDBID 2P16"
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Howdy! If you've gotten this far with your MD project, you've now moved out of the realm of DOCK6 and into the world of molecular dynamics (MD). This tutorial will cover how to use the AMBER 16 software package to simulate your protein-ligand complex on a sub-microsecond timeframe and use the resulting data to calculate binding energies. | Howdy! If you've gotten this far with your MD project, you've now moved out of the realm of DOCK6 and into the world of molecular dynamics (MD). This tutorial will cover how to use the AMBER 16 software package to simulate your protein-ligand complex on a sub-microsecond timeframe and use the resulting data to calculate binding energies. | ||
| − | == '''Preparing the Structure''' == | + | == '''Preparing the Structure''' == |
| − | + | Before you start any preparation, you need to keep yourself organized to make sure that you're running the right files and jobs for your MD simulation, otherwise, it may explode. | |
| + | To do this, you can either copy the example AMBER directory to your scratch directory: | ||
| + | <pre> | ||
| + | /gpfs/projects/AMS536/2023 | ||
| + | </pre> | ||
| + | Or, you can create the following directories: | ||
| + | <pre> | ||
| + | mkdir 000.parameters | ||
| + | mkdir 001.tleap_build | ||
| + | mkdir 002.equilibration | ||
| + | mkdir 003.production | ||
| + | mkdir 004.analysis | ||
| + | mkdir zzz.master | ||
| + | </pre> | ||
== '''Simulation Parameters''' == | == '''Simulation Parameters''' == | ||
Revision as of 14:18, 26 April 2023
Contents
Introduction
Howdy! If you've gotten this far with your MD project, you've now moved out of the realm of DOCK6 and into the world of molecular dynamics (MD). This tutorial will cover how to use the AMBER 16 software package to simulate your protein-ligand complex on a sub-microsecond timeframe and use the resulting data to calculate binding energies.
Preparing the Structure
Before you start any preparation, you need to keep yourself organized to make sure that you're running the right files and jobs for your MD simulation, otherwise, it may explode.
To do this, you can either copy the example AMBER directory to your scratch directory:
/gpfs/projects/AMS536/2023
Or, you can create the following directories:
mkdir 000.parameters mkdir 001.tleap_build mkdir 002.equilibration mkdir 003.production mkdir 004.analysis mkdir zzz.master
