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

[val]

Hi Miguel,
    Google is your best friend.  Try, e.g., google with
'molecule energy software'.
    But i wouldn't rely much on this type of
calculation; it does not help much in answering real
questions in (bio)chemistry and bioinformatics.
my best,
val


----- Original Message -----
From: Miguel Pignatelli
To: bio_bulletin_board at bioinformatics.org
Sent: Thursday, October 30, 2003 4:43 AM
Subject: [BiO BB] Molecular Mechanics (Universal Force Fields models)


Hi,

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