minimax [options...] molecule


Description:

Standalone energy minimizer for the Tripos and CHARMM force fields.


molecule:
Name of the Sybyl MOL2 file (or Sybyl MOL file, if the Tripos force field is used) which contains the molecule to be minimized.  The default file extension is .mol. The molecule file will be overwritten by a new version with the optimized conformation, except if the extension of the input molecule is .min,  in which case a new file with extension .mol will be generated instead.
Options:
Force field selectors:

-taff : use the Tripos force field. The atom types of the input molecule must be valid Tripos atom types. Force field parameters will be read from a set of files in Sybyl's PARAMETER ASCII WRITE format. The location of these files may be specified through the environment variable MINIMAX_FF_TABLES or through the -t option (c.f. below).

-charmm : use the CHARMM (or CHARMm) force field (with some minor restrictions). The atom types of the input molecule must be valid CHARMM (or CHARMm) atom types. This options requires the presence of a file with the molecular topology in CHARMM format (so called PSF file). The name of this file may be specifies with the -psf option (default: molecule.psf). Force field parameters will be read from the file PARM.PRM in the directory defined by the environment variable MINIMAX_FF_TABLES or through the -t option (c.f. below). The -prm option may be used to specify an alternate parameter file.

-amber : use the Amber force field. The atom types of the input molecule must be valid Amber atom types. This option requires the presence of a file with the molecular topology and Amber force field parameters (so called parameter/topology file). The name of this file may be specified with the -prm option (default: molecule.prm).

Note: if no force field selector option is used, -taff will be used by default.
 

General options:

-i <max.iter> : maximum number of iterations (default: 15*number of atoms). If <max.iter> is 0, the energy of the starting conformation will be computed, but no output molecule file will be produced.

-g <acc> : required accuracy of the r.m.s. gradient in mdyn. Default: 0.00035.

-m <method> : method to be used for energy minimization. <method> may be either bfgs [limited memory BFGS mehod, J. Nocedal, Northwestern University], or conjugate [Polak-Ribiere CG a la VA14], or other [Conjugate Gradient, J. Nocedal, Northwestern University]. Default: bfgs, with automatic switch to conjugate if the BFGS method is not available, or if using BFGS would exceed memory limits.

-b : increase initial minimization step in conjugate gradient minimizer. This option may be accumulated, i.e. -bb, -bbbb for increased effect. Note: this would often help if the minimizer fails due to very bad initial geometry in eralier versions of the program. The current version is more robust, and using this option should no longer be necessary.

-c- : suppress computation of electrostatic energy.

-C : constraints (distances, angles, dihedral angles, volume, projection)  are added to the standard energy terms. The definitions of the constraints are read in from the file molecule.con.

-Cf <constraints> : same as -C, but constraints are read from the file <constraints>.

-Cs :  automatically add a chirality constraint to all centers with 4 bonds. The constraint will attempt to preserve the sign of the volume of the tetrahedron generated by the four neighboring atoms.

Exit Status:

Minimax sets the exit status as follows:

0 : success, converged.
1 : input error
2 : no atoms
3 : topology error
4 : missing FF parameters
5 : NB list error
6 : unknown error (check coredump etc)
7 : no convergence
8 : max iter exceeded



A.Widmer, NIBR/CPC/CSG-SB