Programs



Hit Here for access to AMMP and related programs.
The online version of the AMMP Help file will help learning this program.
Hit here (url) to send email to one of the authors. (if the mail fails please hit here ).
AMMP
AMMP is our local molecular mechanics and dynamics program. AMMP is a fully featured molecular modeling program. It features: AMMP is extensively vectorized and runs under UNIX, WINDOWS 3.1 and WINDOWS 95.
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.

rms plot of the run
spacefilling picture of ps-dna
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
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.