Useful links:
Below are tutorials prepared by the Amber developers to help you learn how to use the Amber software suite.
There are also two sets of Japanese versions: one from Akira Wadano and Takenori Kanai, and a second prepared by Conflex corporation.
**Please note that some of these tutorials were written to run quickly for illustrative purposes. You should refer to the manual or a published paper to choose optimal parameters or methods specific to your application.
1 Building Systems 1.1 Using pdb4amber 1.2 Fundamentals of LEaP 1.3 Building a Peptide Sequence 1.4 Building Protein Systems in Explicit Water 1.5 Calculating Salt Molarity in an Explicit Water System 1.6 Hydrogen Mass Repartitioning 1.7 An Amber Lipid Force Field Tutorial: Lipid14 1.8 Simulation of a protein crystal 1.9 Simulations of a room-temperature ionic liquid 1.10 Material systems modeling tutorial 1.11 Using 3D-RISM to place waters 1.12 Building Systems with CHARMM-GUI
2 Developing Nonstandard Parameters 2.1 Simulating a pharmaceutical compound using Antechamber and the Generalized Amber Force Field 2.2 Setting up a DNA-Ligand System 2.3 Building your own Custom Residues (old version) 2.4 Metal Ion Modeling Tutorial 2.5 Generating Force Field Parameters with Paramfit 2.6 Deriving Implicitly Polarized Charges in mdgx 2.7 Deriving bonded parameters with mdgx
3 Running MD 3.1 Equilibration of Explicit Water Systems 3.2 Running MD with pmemd 3.3 Equilibration of Implicit Solvent System (GB)
4 Trajectory Analysis 4.1 An Introduction to CPPTRAJ 4.2 RMSD Analysis in CPPTRAJ 4.3 Analysis of a nucleic acid simulation 4.4 Introduction to Principal Component Analysis with CPPTRAJ 4.6 Combined Clustering Analysis with CPPTRAJ 4.6 Hydrogen Bond Analysis with CPPTRAJ
5 Introductory Case Studies 5.1 Simple Simulation of Alanine Dipeptide 5.2 Simulating a DNA polyA-polyT Decamer 5.3 Simulating the Green Fluorescent Protein and building a modified amino acid residue 5.4 Loop dynamics of the HIV-1 integrase core domain 5.5 Case Study - Folding TRP Cage (Advanced analysis and clustering) 5.6 Using mdgx to manipulate small molecules
6 Sampling Configuration Space 6.1 Replica Exchange 6.2 Conformational equilibria of poly-proline pentamer 6.3 Using Accelerated Molecular Dynamics (aMD) to enhance sampling 6.4 Adaptive Steered Molecular Dynamics 6.5 Conformational equilibria of methyl-alpha-L-iduronic acid in explicit water 6.6 Nudged Elastic Band (NEB) simulations 6.7 The unified “middle” thermostat scheme in AMBER for efficient configurational sampling (ADVANCED)
7 Free Energies 7.1 Molecular Mechanics with a Poisson‐Boltzmann/Surface Area solvent: MM-PBSA 7.2 pKa Calculations using Thermodynamic Integration 7.3 Thermodynamic Integration using soft core potentials 7.4 Umbrella sampling: A Potential of Mean Force in alanine dipeptide Phi/Psi rotation 7.5 Umbrella sampling: Transfering methanol through a membrane 7.6 Free energy estimation for conformers of dialanine using EMIL 7.7 Computing binding enthalpy values 7.8 Free energy calculations with the Free Energy Workflow Tool (FEW) 7.9 Grid Inhomogeneous Solvation Theory for water thermodynamics: in Factor Xa 7.10 Computing Binding Free Energy using the Attach-Pull-Release (APR) Method 7.11 The Nonequilibrium Free Energy (NFE) Toolkit for pmemd
pmemd
8 Chemical Reactions and Equilibria 8.1 Constant pH MD example: Calculating pKas for titratable side chains in Hen Egg-White Lysozyme 8.2 Constant pH and Redox Potential MD example: predicting pH-dependent Eo values 8.3 A simple coupled potential QM/MM/MD simulation. 8.4 Steered molecular dynamics of a proton transfer reaction 8.5 Quantum dynamical effects in liquid water: diffusion and IR spectra
9 NMR Refinement 9.1 NMR Refinement of DNA and RNA Duplexes
10 Tools 10.1 Unix and Editing Commands 10.2 Building Systems - CHARMM-GUI 10.3 VMD Visualization Software 10.4 Chimera Visualization Software 10.5 Plotting 10.6 Jupyter Notebooks and Python 10.7 Course Grain SIRAH
"How's that for maxed out?"
Last modified: Sep 23, 2020
