[Kalzium] About Molecular Viewer

[Geoffrey Hutchison]

>>>> So, I'm asking this because I'm working on a project for conclude  
>>>> my
>>>> graduation in Computer Science at University where I'll have to  
>>>> draw
>>>> the molecule and calculate the energy's minimum for the bonds,  
>>>> angle
>>>> bending, torsions and non-bonded interactions.

Dear Leandro,

What you describe above (calculating the energy) is already what is  
done in Avogadro and Kalzium (4.1). If that's still your project,  
there are other force fields which would be very useful (and  
interesting) to implement. The "force field" is the method to  
calculate the energy for bonds, angles, torsions, and various non- 
bonded interactions.

For example, the three force fields used by Avogadro (UFF -- which is  
used in Kalzium too, MMFF94, and Ghemical) are "all atom" methods. For  
proteins, people sometimes use Amber or CHARMM force fields, which  
consider groups of atoms (residues) at one unit. This is the technique  
used in Folding at Home.

Avogadro has helped with several student projects -- so perhaps we can  
help you too. Why don't you describe your project in more detail. :-)

Cheers,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoffh at pitt.edu
web: http://hutchison.chem.pitt.edu/