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PR540 Lessons on molecular modeling
Click on what you want:
links to packages
use the save file as option on your browser
- Windoz 95 direct access
- Linux AMMP graphical UNIX/Linux sources (works on SGI)
- Linux AMMP non-graphical UNIX/Linux sources
- UNIX/Linux preAMMP You need this to generate
molecular geometry data for the unix/linux AMMP. (unless you're really a masochist).
amino acids with pdb-named hydrogens
a worked example (the course is also a good set of examples)
- hopac.zip direct access
- Windows AMMP help file
- Windows AMMP tricks
- anonymous ftp has been re-opened
The current windows ammp (ammp95.zip) is now 1.3.
AMMP now has atom colors. Try the View|color scheme|color option in the
view window. Atoms can be colored by type, force, and charge. The charge
is especially useful for sorting out interactions. The force color
is useful when modeling. Regions of high residual force are probably wrong.
This is the proper shareware
release. The latest release has a useful help file (almost complete),
improved user interface (you can specifiy parameters for dynamics
and calculating atomic charges, and center on a given atom from the
menu (you could before, but had to type the information)), and mouse
tracking for the coordinate display. Quantum mechanics and protein
folding support are on the way. The file 'example.zip' shows a worked
example where the lambda repressor-dna complex is put into AMMP.
The file 'hopac.zip' gives a worked homology or similarity model and
has the tools for generating such models.
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- Literature citations for AMMP
- in case of difficulty
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