2024 AMBER tutorial 2 with PDBID 1NDV

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Contents

1 Introduction
- 1.1 Getting Started
2 Before Simulation
3 Minimization and Equilibration
4 Production
5 Analysis

Introduction

Getting Started

Before Simulation

Structure

Force Field Parameters

TLEap

Minimization and Equilibration

Production

Analysis

RMSD

Hydrogen Bonding

MM-GBSA

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