Biomedical Engineering Reference
In-Depth Information
since then, and to get started I simply built the molecule onscreen in HyperChem using the
'build' option (Figure 6.2).
Figure 6.2
HyperChem screen grab
You probably noticed the single chiral centre; most packages have an automatic inversion
feature in case you want to switch between D and L forms.
Most packages also give the so-called 'rendering' as an option. I chose 'balls and cyl-
inders' but you can experiment to get whatever pleases you best. There is a choice of
optimization method and a choice of force field. AMBER seemed the appropriate choice
for an amino acid, and I easily located a stationary point with energy 8.678411 kcal mol
−
1
.
This energy is not for direct comparison with experiment; only differences are of any
significance in MM calculations. In this example, I am going to use the energy as a relative
marker in our search for the global minimum.
6.2 Conformation Searches
The stationary point located above is of course a local minimum. Figure 6.3 shows the
results we might expect to find from a conformational search on a (hypothetical) molecule.
