NEIMO calculations were carried out on a wide variety of peptide and
protein systems, ranging from the five-residue peptide Met-enkephalin
to the tomato bushy stunt virus (TBSV) protomer, which contains three
proteins totaling 893 residues. Table 
contains a list of
the ten systems studied. The two peptides were built using the
Peptide Builder of BIOGRAF[37], which uses standard amino
acid geometries. They were initially configured as alpha helices, but
were minimized to a local potential energy minimum using conjugate
gradients minimization. As in all calculations reported here, the
DREIDING forcefield was used for these minimizations. No solvent or counterions
were used, but the dielectric constant for each pair of atoms and
was set proportional to
, the distance between them. This
crudely represents the electrostatic shielding of aqueous solvent.
For these peptides, no nonbond cutoff was used; i.e., all
possible pairs were included in the van der Waals and electrostatic
calculations. The initial conformations of the proteins were derived
from the X-ray crystal structures listed in Table
. All
metal ions, solvent molecules, and disulfide bridges were removed,
leaving only protein chains which conformed to a tree topology. (As
mentioned above, sidechain aromatic rings and proline rings are
treated as single clusters).
Hydrogen atoms were then added to non-carbon atoms. As was
done for the peptides, the DREIDING forcefield was used to
energy-minimize these conformations. Nonbonds, however, were treated
differently. The large size of the proteins precluded the inclusion
of all possible nonbond pairs, a number close to for an
-atom
protein. Therefore, the cell-multipole method (CMM) of Ding et
al.[25] was used to calculate the van der Waals and
electrostatic interactions. This method is roughly proportional to
, but provides far greater accuracy than the standard approach of
excluding all nonbond interactions greater than 9 Å.
