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1.1. Information flow in Amber
pdb4amber generally helps in preparing pdb-format files coming from other places (such as rcsb.org) to be com-
patible with LEaP.
parmed provides a simple way to extract information about the parameters defined in a parameter-topology file. It
can also be used to check that the parameter-topology file is valid for complex systems (see the checkValidity
command), and it can also make simple modifications to this file very quickly.
antechamber is the main program to develop force fields for drug-like molecules or modified amino acids using
the general Amber force field (GAFF). These can be used directly in LEaP, or can serve as a starting point
for further parameter development.
MCPB.py provides a means to build, prototype, and validate MM models of metalloproteins and organometallic
compounds. It uses the bonded plus electrostatics model to expand existing pairwise additive force fields.
It is a reimplementation of MCPB in Python, with a more efficient workflow and many modeling processes
from previous versions incorporated automatically.
IPMach.py provides a tool to facilitate the parameterization of nonbonded models (12-6 LJ model and 12-6-4
LJ-type model) for ions.
paramfit allows the generation of bonded force field parameters for any molecule by fitting to quantum data.
packmol-memgen provides a simple way to generate membrane systems, with or without protein, by orient-
ing input proteins with Memembed and using Packmol as the packing engine. It can handle complex
lipid mixtures, as well as multi-bilayer systems. The output is compatible with Amber through charmm-
lipid2amber.py.
1.1.2. Simulation programs
sander (part of AmberTools) is the basic energy minimizer and molecular dynamics program. This program
relaxes the structure by iteratively moving the atoms down the energy gradient until a sufficiently low average
gradient is obtained. The molecular dynamics portion generates configurations of the system by integrating
Newtonian equations of motion. MD will sample more configurational space than minimization, and will
allow the structure to cross over small potential energy barriers. Configurations may be saved at regular
intervals during the simulation for later analysis, and basic free energy calculations using thermodynamic
integration may be performed. More elaborate conformational searching and modeling MD studies can also
be carried out using the sander module. This allows a variety of constraints to be added to the basic force
field, and has been designed especially for the types of calculations involved in NMR, Xray or cryo-EM
structure refinement.
pmemd (part of Amber) is a version of sander that is optimized for speed and for parallel scaling; the pmemd.cuda
variant runs on GPUs. The name stands for “Particle Mesh Ewald Molecular Dynamics,” but this code can
now also carry out generalized Born simulations. The input and output have only a few changes from sander.
mdgx is a molecular dynamics engine with functionality that mimics some of the features in sander and pmemd,
but featuring simple C code and an atom sorting routine that simplifies the flow of information during force
calculations. The principal purpose of mdgx is to provide a tool for redesign of the basic molecular dynamics
algorithms and models, and for supporting new models for parameter development.
NAB (Nucleic Acid Builder) is a language that can be used to write programs to perform non-periodic simulations,
most often using an implicit solvent force field.
1.1.3. Analysis programs
mdout_analyzer.py is a simple-to-run Python script that will provide summaries of information that is in the
output files from sander or pmemd.
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