AMMP Home Page

Welcome to AMMP

AMMP is a modern full-featured molecular mechanics, dynamics and modeling 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 program and modeling methods are under active development. User feedback is appreciated and incorporated in the program. A graphical interface is available for Linux and Unix with the openGL graphics language and for windows 95/98/NT

You might want to see:

Download information

The links to the files below use the http server to load the files to your machine.

What's New!

  • GTK+ version for linux
    The graphical linux version of AMMP is being rebuilt with GTK/GDK. This is resulting in improved program stability, program performance, and a vastly improved user interface. The program is still in beta but the current working version is worth a look. It requires GTK 1.0-1.2 and will run on default installations of Red Hat Linux 5.2 and up.
  • sequence_remap windows executable.
  • the sources of sequence_remap for real computers.
  • The OBSOLETE homology mapping program newho is here (source only).
  • Density functional methods
    Density functional quantum mechanics integration with molecular mechanics. The paper has finally made it into press, so this feature is now available. As usual the manuals are behind, but send email to me if you want to try it out. The feature has been there for some time, but completely undocumented and unannounced so you don't need to download new versions (yet).
  • Neural Network Polymer Modeller
    A randomized neural network modeller for polymer structure has been implemented and the algorithm described in a paper accepted by the Journal of Mathematical Chemistry. The algorithm will build self-avoiding polymers which obey distance constraint data. Invoke it with "kohonen nstep radius (-1 to keep going | 1 to re-initialize);". It uses the potentials you've defined so remember to use the "use" command to set the ones you want (i.e. its probably a good idea to turn off the nonbonded terms -which are not needed and expensive).
  • Improved distance geometry type the command dgeom #of_cycles> and stand back.

Linux and Unix Versions

  • All the UNIX/Linux distributions now include both the graphical and non-graphical versions of AMMP. Executable images and all required programs are included in each release distribution.
    use the save file as option on your browser
  • latest sources (non graphical)
  • New release version using GTK+/GDK (requires GTK+ 1.0 and up). Does not include Preammp Untar and type 'make'.
  • Preammp latest version. The current atoms file is atoms.tuna, and the new_charge directory is the best for proteins.
  • from here on the versions are OBSOLETE
  • Linux/Unix Graphical version as an i386.rpm requires Mesa(OGL) and Lesstif(motif) This is an obsolete version, still listed here for completeness.
  • Linux AMMP binaries including the Lesstif library.
  • Linux AMMP latest non-graphical version (source only)
  • AMMP Linux/UNIX sources. This will build on SGI/Alpha and other machines as well as Linux.
  • AMMP binaries for SGI. This will run on SGI-Irix 5.3 and up.
  • New release version using GTK+/GDK (requires GTK+ 1.0 and up). Does not include Preammp (see next item).
  • UNIX/Linux preAMMPPreammp is used to molecular geometry data for the unix/linux AMMP(unless you're really a masochist). Preammp is now included in the Linux/Unix sources and distirbution so you no longer need to download this. However if you need it, here it is.
  • HTML help files

Windows Version


use the save file as option on your browser

Useful Stuff


use the save file as option on your browser

Comments, likes, dislikes, pet peeves?

If you're checking out our software, we'd like to know who you are and what you find interesting. This information is, of course, purely voluntary. However, we are dependent on grant funding, and it greatly helps to be able to cite specific numbers of people. Clicking on the submit button sends email, which may or may not be obvious to you.
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