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The molecular structure (.smol) file

This file contains information on molecular structure, partial atomic charges and the force field atom types. All the lines beginning with ``#'' are considered as commentaries. The first non-commentary line defines the number of atoms in the molecule. Then follows the corresponding number of lines describing each atom. Each line consists of 6 parameters. The first one is the name of the atom. Parameters 2 - 4 are the initial X, Y and Z coordinates of atoms. The 5-th parameter is the partial atom charge, and the 6th parameter is the force field atom type. Makemol just rewrites parameters 1-5 into corresponding sections of the .mmol file, and uses the force field atom type (6th parameter) in order to find the force field parameters from the .ff file.

Makemol defines masses from the begin_definitions section of the force field file, and if it is not present, from the one or two first letters in the atom name (the first column of .smol file). If the program cannot recognize the element, it complains about that; in such a case the mass of the atom must be put manually into resulting .mmol file.

After the description of atoms, a section describing the bond structure follows. The first line of this section is the number of bonds. Then the corresponding number of lines follows, with two numbers in each line defining numbers of atoms bound by the corresponding bond. From this list, Makemol builds lists of covalent angles and torsions angles, and substitute the corresponding force field parameters.


next up previous contents
Next: Tranal utility Up: Makemol utility Previous: char2mdx   Contents
Alexander Lyubartsev 2015-02-06