sci-chemistry@gentoo.org
Gentoo Chemistry Project
A fortran program for the calculation of some eigenvectors of a large real,
symmetrical, matrix.
If the matrix was obtained, for instance, with the PDBMAT program, these
eigenvectors correspond to the low-frequency normal modes (i.e., mostly
those with a collective character) of the system. Note that in the case of
proteins, low-frequency normal modes thus obtained are found to be very close
to those obtained with standard, much more realistic (e.g., all atoms with
empirical force fields), models.
The method used rests upon the RTB approximation (standing for
Rotations-Translations-of-Blocks). Within the frame of this approximation,
blocks of n (n=1,2,...) consecutive monomers (amino-acid residues) are
assumed to behave like rigid bodies.
Requirements: a matrix in the "i j non-zero-ij-matrix-element" format.
A file with the coordinates of the system, in the PDB or "x y z mass
block-number" format.