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General organization

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:

Usage:

makemol <mol structure file> <force field file>

The format of molecular structure file is determined by the file name extension.


next up previous contents
Next: The force field (.ff) Up: Makemol utility Previous: Makemol utility   Contents
Alexander Lyubartsev 2015-02-06