background image
c CCLRC
Section 4.3
by hand. Otherwise, the input of force field data for crystalline systems is particularly simple,
if no angular forces are required (notable exceptions to this are zeolites and silicate glasses - see
below). Such systems require only the specification of the atomic types and the necessary pair
forces. The reader is referred to the description of the DL POLY 3 FIELD file for further details
(Section
5.1.3
).
DL POLY 3 can simulate zeolites and silicate (or other) glasses. Both these materials require the
use of angular forces to describe the local structure correctly. In both cases the angular terms
are included as three body terms, the forms of which are described in Chapter
2
. These terms are
entered into the FIELD file with the pair potentials.
An alternative way of handling zeolites is to treat the zeolite framework as a kind of macromolecule
(see below). Specifying all this is tedious and is best done computationally: what is required is to
determine the nearest image neighbours of all atoms and assign appropriate bond and valence angle
potentials. What must be avoided at all costs is specifying the angle potentials without specifying
bond potentials. In this case DL POLY 3 will automatically cancel the non-bonded forces between
atoms linked via valence angles and the system will collapse. The advantage of this method is that
the calculation is likely to be faster than using three-body forces. This method is not recommended
for amorphous systems.
4.3.2
Macromolecules
Simulations of proteins are best tackled using the package DLPROTEIN [
42
] which is an adap-
tation of DL POLY specific to protein modelling. However, you may simulate proteins and other
macromolecules with DL POLY 3 if you wish. This is described below.
If you select a protein structure from a SEQNET file (e.g. from the Brookhaven database), use
the utility proseq to generate the file CONFIG. This will then function as input for DL POLY 3
. Some caution is required here however, as the protein structure may not be fully determined and
atoms may be missing from the CONFIG file.
If you have the "edit.out" file produced by AMBER for your molecule use this as the CON-
NECT DAT input file for the utility ambforce. ambforce will produce the DL POLY 3 FIELD
and CONFIG files for your molecule.
If you do not have the "edit.out" file things are a little more tricky, particularly in coming up with
appropriate partial charges for atomic sites. However, there are a series of utilities that will at least
produce the CONNECT DAT file for use with ambforce. We now outline these utilities and the
order in which they should be used.
If you have a structure from the Cambridge Structural database (CSDB) then use the utility
fraccon to take fractional coordinate data and produce a CONNECT DAT and "ambforce.dat"
file for use with ambforce. Note that you will need to modify fraccon to get the AMBER names
correct for sites in your molecule. The version of fraccon supplied with DL POLY 3 is specific
to the valinomycin molecule.
If you require an all atom force field and the database file does not contain hydrogen positions then
use the utility fracfill in place of fraccon. fraccon produces an output file HFILL which
should then be used as input for the utility hfill. The hfill utility fills out the structure with
the missing hydrogens. (Note that you may need to know what the atomic charges are in some
systems, for example the AMBER charges from the literature.)
Note: with minor modifications the utilities fracfill and fraccon can be used on structures
from databases other than the Cambridge structural database.
69