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The makemol utility is used to generate a .mmol file
(containing information on both molecular structure and the force field)
from two files: a force field (.ff) file, with information about
force field parameters, and a molecular structure file (.smol or
.mol2), which
contains only structural information about the molecule (initial atom
coordinates, the partial atomic charges, the force field atom types
(which should match the types in the force field file) and
the list of covalent bonds.
The utility constructs the list of covalent angles and torsion angles,
and pick up the force field parameters from the force field file. If some
parameters are not found in the force field file, the corresponding line
in the resulting .mmol file is marked with an exclamation mark,
and a note is written on the screen and in the makefile.log file.
The list of Improper torsions is not generated automatically. If impropers
exist for the given molecule, they should be added into .mmol file
manually.
The molecular structure file can be in one of four formats and have the corresponding file name extension:
.smol : MDynamix simple molecular format, explained below
.mol2 : TRIPOS .mol2 format, compatible with output of
Avogadro molecular editor and Antechamber utility of AmberTools.
.alc : Alchemy-like format (depreciated)
.crd : Old Charmm .crd format (depreciated)
Usage:
makemol <mol structure file> <force field file>
The format of molecular structure file is determined by the file name extension.