[BiO BB] Molecular Mechanics (Universal Force Fields models)

Miguel Pignatelli Pignatelli at noraybio.com
Thu Oct 30 04:43:03 EST 2003


I'm trying to make a program in C that calculates the energy of a molecule from the coordinates X,Y,Z of its atoms. We want to apply the Universal Force Fields (UFF) described by Rappe. Once we have the total energy of the molecule (contribution from each chemical bond (bond stretching), angle bending, torsional terms, improper torsions, out of plane bending motions and non-bonded interactions (electrostatic and Van der Waals forces)) we will look for energy minimisation through the conjugate gradient minimisation method.

I am looking for a similar software to look at or any algorithm that could help me. First of all I would like to know what is the best data structure to use in this kind of software and if there is any similar software to look at its code or any algorithm that implements the UFF.
The software imput will be atoms and coordinates, so it will determine which atoms are bonded. Is there any efficient algorithm for that?
Any suggestions?

Thanks all
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