Zmin

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zmin is a top level plop command used to perform z-matrix minimization. It is unknown if this ever worked.

[edit] Z-Matrix Minimization

The usual minimization is performed in Cartesian coordinates, which makes it difficult to constrain bond lengths, angles, or dihedral angles. Z-matrix minimization is typically less efficient for proteins, but can be very efficient for peptides, and makes it easy to constrain elements of the Z-matrix (bond lengths, angles, dihedrals). The entire peptide/protein is minimized with this command; it is not possible to freeze (in Cartesian space) parts of the structure. The command structure is

zmin  &
omit bond [none,all,atom identifier] &
omit angl[e] [none,all,atom identifier] &
omit tor[sion] [none,all,atom identifier] &
[followed by any other minimization options, described at minimize]

The “omit” options must come before any others, and indicate what elements of the Z-matrix should be constrained. “omit bond all”, for example, would keep all bond lengths fixed. To specify specific elements of the Z-matrix to omit, you have to know how it’s constructed (it starts from the N-terminus of the protein). “omit angle A:2:N” would indicate that the angle defined by A:2:N and the two atoms preceding it in the Z-matrix should be omitted.

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