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Another Molecular Mechanics Program

AMMP is a modern full-featured molecular mechanics, dynamics and modelling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features, like numerically stable molecular dynamics, fast multipole method for including all atoms in the calculation of long range potentials and robust structural optimizers, it has a flexible choice of potentials and a simple yet powerful ability to manipulate molecules and analyze individual energy terms. One major advantage over many other programs is that it is easy to introduce non-standard polymer linkages, unusual ligands or non-standard residues. Adding missing hydrogen atoms and completing partial structures, which are difficult for many programs, are straightforward in AMMP. It is written in C and has been ported to many different computers. The source code is available under the GNU "copyleft" so that it is easy to follow exactly what the program is doing. Another major advantage over commercial software is that AMMP can be easily included in another program to supply molecular mechanics function.
The main features implemented in AMMP are:

  • Energy minimization (steepest descent, conjugate gradients, quasi-Newton, truncated Newton, trust-region and genetic algorithms). 
  • Molecular dynamics.
  • Rigid molecular docking (genetic algorithm based).
  • Fast long range electrostatics and non-bonded terms. AMMP runs without cutoffs in times comparable to or better than an 8 Angstrom cutoff in other programs.
  • Stable, numerically accurate, molecular dynamics. AMMP is stable with difficult problems such as parallel stranded DNA. (shown with its Na counterions below).
  • Flexible choice of potential functions. In addition to standard formulations, AMMP has non-point charges, explicit Debye screening, accurate polarization models, non-harmonic bond and angle formulations, and coupled bond-angle terms available.
  • Calculates partial charges for new molecules.
  • Embedding and homotopy methods for rapid model building.
  • Neural network polymer modeller (Kohonen neural network).
  • Self-contained, and can be embedded in other programs.

AMMP VE (VEGA Edition) is a modified version of the original AMMP project developed by Robert W. Harrison (for more information, see the original Web site). The new features included in the VE edition

  • Conformational search (grid scan, random and Boltzmann jump).
  • Some code improvements to make it faster.
  • VEGA ZZ interface.


Current release: 2.4.0
Latest update: 10/07/2012

The Windows 32 and 64 bit versions are included in the latest VEGA ZZ package and so if you want to use these operating systems, it's strongly recommended to download that distribution (for more details, go to the VEGA ZZ main site).
If you need the source code or other binaries, please download the following package:

 AMMP VE 2.4.0 Full Package 

Included in this package:

  • Windows x86 (32 bit) and x64 (64 bit) binaries.
  • Linux x86 (32 bit), x64 (64 bit) and ARM with VFP binaries.
  • Source code in standard ANSI C.
  • Examples.
  • HTML manual.
  • This release includes the Linux executable optimized for Rasperry Pi.