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1 Building Systems

1.1 Using pdb4amber

flow This page highlights the existence of pdb4amber, the recommended method for preparing a pdb file for use in LEaP. This program was written by Romain Wolf and modified later mainly by Hai Nguyen.

1.2 Fundamentals of LEaP

This tutorial demonstrates rudimentary system building in LEaP, the main program for preparing simulations in AMBER. The tutorial serves as a nice reference for different kinds of files used in the LEaP program, introduces the workflow, and provides a simple example of building a protein in water.

By Pengfei Li and David Cerutti

1.3 Building a Peptide Sequence

flow This tutorial utilizes the sequence command within LEaP to build an extended structure of the 10 amino acid chignolin. It also sets up a topology file and starting coordinates for an implicit solvent calculation with the GBneck2 parameters.

By Jan Ziembicki and Maria Nagan

1.4 Building Protein Systems in Explicit Water

This tutorial will go over how to build an explicitly solvated protein system in LEaP. First, users will use basic features in VMD to examine a protein structure. Because preparing experimentally-determined protein structures for simulations are not straightforward, this tutorial will also help users evaluate and change the pdb file as necessary. Finally, users will use LEaP to build a protein system in explicit solvent including counterions and a buffer of ions.

By Abigail Held and Maria Nagan

1.5 Calculating Salt Molarity in an Explicit Water System

This tutorial show users how to calculate the number of buffer ions to add in LEaP based on an overall molarity and the volume of a truncated octahedral box of explicit water.

By Abigail Held and Maria Nagan

1.6 Hydrogen Mass Repartitioning

This tutorial shows how to use parmed to repartition the hydrogen atomic masses. This work is based on Adrian Roitberg's work.

1.7 An Amber Lipid Force Field Tutorial: Lipid14

lipid bilayer Updated for Lipid14: Phospholipid bilayers are essential components to cellular membranes and are the stage where many essential biophysical and biochemical processes take place. This tutorial explains how to set up and simulate lipid bilayers with the Lipid14 force field. A DOPC bilayer is built, converted, and loaded into LEaP to assign parameters for molecular dynamics simulation. A molecular dynamics scheme is presented followed by analysis of the bilayer structural properties in the trajectory. Furthermore, membrane-bound proteins are examined and a simple membrane-bound protein system is built.

By Ben Madej and Ross Walker

Parker de Waal has created an alternative lipid-building tutorial using Maestro.

1.8 Simulation of a protein crystal

Protein crystal simulation
This tutorial describes one way to set up a simulation of a protein crystal, showing how to construct unit cells, and how to fill in missing solvent.

By David Cerutti

1.9 Simulations of a room-temperature ionic liquid

ionic liquid This tutorial illustrates the use of antechamber and sander to carry out some simple simulations of a room-temperature (non-biological!) ionic liquid.

By Chris Lim

1.10 Material systems modeling tutorial

material in water Together with the INTERFACE force field, this tutorial explores the functions of employing the AMBER software package to modeling material and interfacial systems.

By Pengfei Li

1.11 Using 3D-RISM to place waters

3D rism toc image This tutorial shows how the 3D-RISM method can be used to generate an initial configuration of water around a solute molecule.

By Daniel Sindhikara

1.12 Building Systems with CHARMM-GUI

Some people find it easier to set up a system for simulation in Amber using the CHARMM-GUI interface. These tutorials were written by Wonpil Im at Lehigh University. He also has YouTube videos.

"How's that for maxed out?"

Last modified: Sep 23, 2020