Difference between revisions of "2021 AMBER tutorial 3 with PDBID 1S19"
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Stonybrook (talk | contribs) (Created page with "In this tutorial, we will be modeling the dynamics of the ligand with the receptor using AMBER 16. Amber is a molecular dynamics simulation software package. = Generating Pa...") |
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| − | In this tutorial, we will be modeling | + | 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 simulation = | = Generating Parameters for the simulation = | ||
Revision as of 14:35, 31 March 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.
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.
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