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ZMM is a
molecular modeling program for theoretical studies of systems of any
complexity: small molecules, peptides, proteins, nucleic acids, and
ligand-receptor complexes.
ZMM searches
optimal structures in the space of generalized coordinates: torsion angles,
bond angles, bond lengths, positions free molecules and ions, and
orientation of free molecules. Any generalized coordinate may be kept
fixed. Molecules and fragments that are not expected to undergo significant
conformational changes may be treated as rigid bodies.
Popular
molecular modeling programs usually work in the space of Cartesian
coordinates of atoms. During energy minimization of a big system, many
Cartesian coordinates-variables move collectively. For example, rotation of
a benzene ring around the C-Ph bond in the Cartesian-coordinates space
involves collective motion of 33 variables. In the generalized-coordinates
space, this rotation involves variation of just one torsion angle. In ZMM,
any fragment of a molecular system may be treated as either rigid or
flexible. The generalized-coordinates method saves large computational
resources if only a small part of a system is considered flexible. Examples
are ligand-protein and protein-protein interactions. The savings occur
because the sampling space is reduced and because molecular interactions
within rigid fragments are not computed.
· ZMM
runs on Windows 2000, XP, 7, 10, Mac-OS, UNIX, and Linux
· ZMM
can be used via the command-line interface
· ZMM can
also be used at Windows via a graphical user interface
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