for access to AMMP and related programs.
The online version of the
AMMP Help file
will help learning this program.
to send email to one of the authors.
(if the mail fails please hit here ).
AMMP is our local molecular mechanics and dynamics program.
AMMP is a fully featured molecular modeling program.
AMMP is extensively vectorized and runs under
WINDOWS 3.1 and
- Fast long range electrostatics and nonbonded 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
- Embeding and homotopy methods for rapid model building.
- Self-contained, and can be embeded in other programs
- Highly parallel version available with PVM
- Literature citations for AMMP
- Quality of the AMMP sp4 potential set
- Quality of the AMMP sp5 potential set
- Nifty windows tricks with AMMP
Data for small molecules can be found at
NIST. Thermochemical and IR spectral data are used for checking the classical force field in AMMP.
Conservation of structure during long molecular dynamics
| HIV protease Crystal Structure|| HIV protease average over 590 ps
AMMP with the sp4 potential set
conserves structure. The average structure for a model of the HIV protease
complex with Indanovir has essentially the same structure as the crystal
structure. The calculation was performed with constant pressure/temperature
dynamics on 9582 atoms without cutoff's. The linux version of
AMMP was used on a pentium II 300 mhz machine and required 45 cpu minutes
per ps. The total elapsed time was a little over two weeks.
Parallel Stranded DNA hairpin with Na counterions
(Courtesy of Dr. Marcus Germann).
AMMP correctly predicts that parallel stranded DNA hairpins are stable.
This model included the DNA, counterions and 1500 waters for
a total of 5150 atoms.
Dynama is a fast docking program which uses the FFT to calculate
the interaction energy between two molecules without cutoffs or other
aphysical approximations. Dynama is able to treat flexability in the
ligands. Dynama can approximations to the the partition function so that
free energies of solvation and solvent exclusion effects can be included
in a screening calculation.