Biomedical Engineering Reference
In-Depth Information
2. An attempt was made to include solvent effects by inclusion of the Coulomb term with
a distance-dependent relative permittivity.
3. The AMBER force field is a 'united atom' one, and hydrogen atoms bonded to car-
bons are not explicitly included. They are absorbed into the atom type parameters for
neighbouring atoms.
4. Lone pairs were explicitly included for sulfur hydrogen bonding.
There are a number of different versions of AMBER; the original united atom version
was later extended to include all atoms. Just to give you a flavour, one modern software
package has the following choices.
1. Amber 2
2. Amber 3
3. Amber for saccharides
4. Amber 94
5. Amber 96.
4.8.5 OPLS (Optimized Potentials for Liquid Simulations)
Like AMBER, OPLS is designed for calculations on amino acids and proteins. The easi-
est thing is for me to quote part of the abstract to the keynote paper (Jorgensen and
Tirado-Rives 1988).
A complete set of inter molecular potential functions has been developed for use in computer
simulations of proteins in their native environment. Parameters have been reported for 25
peptide residues as well as the common neutral and charged terminal groups. The potential
functions have the simple Coulomb plus Lennard-Jones form and are compatible with the
widely used models for water, TIP4P, TIP3P and SPC. The parameters were obtained and
tested primarily in conjunction with Monte Carlo statistical mechanics simulations of 36 pure
organic liquids and numerous aqueous solutions of organic ions representative of subunits in
the side chains and backbones of proteins ...
Improvement is apparent over the AMBER united-atom force field which has previously
been demonstrated to be superior to many alternatives.
I will explain about TIP and Monte Carlo in later chapters. Each atomic nucleus is an
interaction site, except that CH
n
groups are treated as united atoms centred on the carbon.
Hydrogen bonds are not given any special treatment, and no special account is taken of
lone pairs.
4.8.6
Johnson
I mentioned earlier the existence of a number of specialist force fields. To take an even
more extreme example, the Johnson force field (Johnson 1964) is specific to solid-state
models involving the pure elements Fe, W and V. The pair potential terms are written
b
1
)
3
U
=
a
1
(
R
−
+
c
1
R
+
d
1
if ε
1
<
R
<ε
2
b
2
)
3
=
a
2
(
R
−
+
c
2
R
+
d
2
if ε
2
<
R
<ε
3
(4.23)
b
3
)
3
=
a
3
(
R
−
+
c
3
R
+
d
3
if ε
3
<
R
<ε
4
=
0if ε
4
<
R
