makemol.readme

分子动力学模拟程序

Makemol - utility to make .mol files

1. Introduction.
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Utility Makemol is intended to create file describing a molecule (.mol) for 
the MDynaMix program from the two files: simple molecule file and force 
field file.

Simple molecule file (.smol) contains information on all atom coordinates 
in the molecule, atomic names, charges and connectivity (bond) list.
Force field file contain information about force field parameters.
The utility create lists of covalent angles and torsions; finds force
field parameters for all covalent bonds, angles and torsion angles, as
well as non-bonded interaction paramater, and create .mol file.

2. Format of simple molecular file.
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Lines beginning with "#" or "*" are commentaries. 

First non-commentary line is the number of atoms.
Then lines for each atom follows.
Each line consists of 6 fields:
1 - name of atom 
2,3,4 - X,Y,Z coordinates in