1 Building Systems
1.1 Using pdb4amber
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
 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
1.7 An Amber Lipid Force Field Tutorial: Lipid14
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
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
1.10 Material systems
modeling tutorial
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
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.
| 
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.
This tutorial shows how to use parmed to repartition the hydrogen atomic masses.
This work is based on Adrian Roitberg's work.
This tutorial illustrates the use of