2023 AMBER tutorial 2 with PDBID 3WZE

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Revision as of 15:45, 5 May 2023 by Stonybrook (talk | contribs) (Directory Setup)
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Introduction

Directory Setup

As always, we set up folders to keep us organized as we move generate files:

mkdir 001_structure
mkdir 002_parameters
mkdir 003_leap
mkdir 004_equil
mkdir 005_production

3WZE Structures

Receptor

Ligand

Amber Simulation Parameters

Tleap

Equilibration

Production

MD Analysis

RMSD

Hydrogen Bonding

MM-GBSA