Difference between revisions of "2021 AMBER tutorial 3 with PDBID 1S19"
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In this tutorial, we will be modeling ligand binding to our receptor using AMBER 16, a molecular dynamics simulation software package created in part by our very own Carlos Simmerling. | In this tutorial, we will be modeling ligand binding to our receptor using AMBER 16, a molecular dynamics simulation software package created in part by our very own Carlos Simmerling. | ||
| − | = Generating Parameters for the | + | = Initial Structures = |
| + | |||
| + | = Generating Parameters for the Simulation = | ||
In order to utilize Amber for molecular dynamic, parameters for the bio molecules will be needed. Luckily, there have been years of parameter development so parameters for the protein do not have to worried about. However, the small ligand does not have parameters in the standard protein force field. Consequently, we will need to generate a fcmod file specific for the ligand. | In order to utilize Amber for molecular dynamic, parameters for the bio molecules will be needed. Luckily, there have been years of parameter development so parameters for the protein do not have to worried about. However, the small ligand does not have parameters in the standard protein force field. Consequently, we will need to generate a fcmod file specific for the ligand. | ||
| − | = | + | = Building the System with TLeap = |
| + | |||
| + | |||
| + | = Equilibration = | ||
| + | |||
| + | == Input Files == | ||
| + | |||
| + | == Run Script == | ||
| + | |||
| + | = Produduction = | ||
| + | |||
| + | == Input File == | ||
| + | |||
| + | == Run Script == | ||
| + | |||
| + | = Analysis = | ||
| + | |||
| + | == RMSD == | ||
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| + | == Hydrogen Bonds == | ||
| + | |||
| + | == MMGBSA == | ||
Revision as of 18:39, 1 April 2021
In this tutorial, we will be modeling ligand binding to our receptor using AMBER 16, a molecular dynamics simulation software package created in part by our very own Carlos Simmerling.
Contents
Initial Structures
Generating Parameters for the Simulation
In order to utilize Amber for molecular dynamic, parameters for the bio molecules will be needed. Luckily, there have been years of parameter development so parameters for the protein do not have to worried about. However, the small ligand does not have parameters in the standard protein force field. Consequently, we will need to generate a fcmod file specific for the ligand.
