2021 AMBER tutorial 3 with PDBID 1S19

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Revision as of 19:39, 1 April 2021 by Stonybrook (talk | contribs) (Generating Parameters for the simulation)
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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.

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.

Building the System with TLeap


Input Files

Run Script


Input File

Run Script



Hydrogen Bonds