AMMP

The AMMP application was developed to be 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.

AMMP only understands its own language. You read an existing coordinate file by compiling it into AMMP language. The program preammp (prewin) does this. Preammp can be run on its own, or called from the file menu in AMMP95.

Preammp requires several inputs. You will be prompted for each of them with a Windows file choice menu. If you dont like this simply cancel the window and enter the filename in the prewin man window (this is simpler to do than to describe!). When you dont have a file, such as when generating coordinates from scratch you will need to both cancel the windows file choice menu and then enter return for the main window.

Preammp only works one residue at a time. YOU WILL NEED TO SUPPLY THE INTERMONOMER Linkage IN A POLYMER. Scripts such as peplink.amp (for proteins) and ndick.amp (for standard DNA/RNA linkage) are supplied. These were generated by generating the template for the dimer and extracting the appropriate terms. They are also a good place to see how to manipulate atoms and potentials in an automatic script.

To Create a new molecule you have to first define a tem