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<DIV><FONT face=Arial size=2>Hi,</FONT></DIV>
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<DIV><FONT face=Arial size=2>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.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>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.</FONT></DIV>
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<DIV><FONT face=Arial size=2>The software imput will be atoms and coordinates,
so it will determine which atoms are bonded. Is there any efficient algorithm
for that?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Any suggestions?</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial><FONT size=2>Thanks
all</FONT></FONT></DIV></FONT></DIV></BODY></HTML>