Description:
Standalone energy minimizer for the Tripos and CHARMM force fields.
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.
-n <non_bonded_cutoff> : non bonded cutoff on
a per
atom basis (default: no cutoff). The argument of this option has the
form cutoff-switch+margin,
where cutoff is the distance beyond which non bonded energy
terms
will be neglected, switch is the switching distance (default:
1
Å), and margin is the non bonded list inclusion margin
(default
1 Å).
-p <nproc> : number of processors for concurrent runs.
On SGIs, this is an upper limit. The number of processors will be
dynamically
adjusted depending on system load.
-P <nproc> : similar to -p, but <nproc> is not dynamically adjusted. This may lead to very bad performance if gang scheduling is not turned off (c.f. pe_environ(5)).
-r <iter> : writes the energy of the current conformation to the output file molcule.dat and to the log file (terminal, in interactive mode) after every <iter>-th iteration.
-s : if this option is set, the molecule is saved after each energy report.
-t <directory> : By default, minimax reads force field parameters from files in the directory defined by the environment variable $MINIMAX_FF_TABLES. A different parameter set may be selected through the -t option. Parameter files for the Tripos force field may be produced with PARAMETER ASCII WRITE in Sybyl.
-X : dump current coordinates to stdout at end of each energy report. This option may be used by graphics front end programs to update the display with new conformations while the energy minimization is on-going.
-xrq <xrq-file> : produces an output file containing 1 record per atom as follows:
(1) (2) (3) (4) (5) (6) (7) (8)(9)(10)(11) (12)
Awkers beware : the record is written by the
FORTRAN format
Tripos FF specific option:
-h <scale> : the sum of the van der Waals radii for
hydrogen
bonding donor / acceptor pairs will be multiplied by this value.
(default:
0.70) .
CHARMM specific options:
-nbx <nbxmod> : sets the non bonded exclusion
mode.
Allowed values and corresponding actions are as follows:
-e14 <e14fac> : scale factor for 1-4 electrostatic interactions (only used if | nbxmod | = 5).
-vsh or
-vsw : select shifting (-vsh) or switching (-vsw)
for the van der Waals interaction when a cutoff (-n) is
used.
The switching function is the same as the one used for switching
electrostatic
interactions. Shifting is implemented through an additive term, such
that
the modified vdW energy and the 1st derivative vanish at the cutoff.
Default: -vsw.
-prm <prmfile> : define alternate parameter file. If <prmfile> is specified without a directory path, the file will be read from the force field parameter directory (c.f. -t option), if the file exists, or from the current working directory. Default: PARM.PRM (i.e. read file from force field directory).
-psf <psf-file> : define topology (PSF) file. Default: molecule.psf.
Amber specific options:
-prm <prmtopfile> : define parameter/topology file. Default: molecule.psf. The file must conform to Amber 6 specifications.
-scee <constant> : 1-4 electrostatic interactions are divided by <constant>. The 1991 and previous force fields used 2.0, while the 1994 force field uses 1.2. Default 1.2.
-scnb <constant> : 1-4 vdw interactions are divided by <constant>. Default 2.0.
-esh or
-esw : defines how the electrostatic energy is modified when
a cutoof (-n) is used. If -esh is used, interactions at
distances
shorter than cutoff will be multiplied by a distance dependent
shifting
factor (1.0 at distance 0, 0.0 at cutoff), which will bring the
electrostatic energy contributions smoothly to zero at the cutoff. If -esw
is used, the interactions within switching distance of the cutoff
(c.f. -n option) will be multiplied by a switching factor (1.0
at cutoff-switch,
0.0 at cutoff). Default: -esw.
-vsh or
-vsw : select shifting (-vsh) or switching (-vsw)
for the van der Waals interaction when a cutoff (-n) is
used.
The switching function is the same as the one used for switching
electrostatic
interactions. Shifting is implemented through an additive term, such
that
the modified vdW energy and the 1st derivative vanish at the cutoff.
Default: -vsw.