Force Field Association
The association of molecular mechanics types is a process that cannot be completely automated.
Although we tried to make it as simple as possible, it should be
always controlled by the user.
The model association with a force field is based on the assignment of each atom to a molecular
mechanics type. The atomic type defines the force field parameters to be used in calculations
of forces exerted on it. Since different force fields are described by different force
parameters and different molecular mechanics types, a mechanism is required to associate atoms
with types and partial charges for each supported force field.
The problem of correct association is complex since there are many molecular mechanics types.
Our approach to the problem relies on the following. Molecular models are built from fragments
(molecules and residues) present in our database. In these fragments, all atoms are described by
Fine types. A Fine type is the most
specific (the most detailed) molecular mechanics type of atoms. Basically, each atom in each
fragment can have an unique Fine type. There are tables that
specify molecular mechanics types and partial charges for a given Fine type
and force field. These tables are included in the mlm format.
Let us consider the following record as an example.
Here, four carbohydrate types were described. They were associated with two types of the
AMBER94 force field and two types of the OPLS force field. Note that four types are reduced
to two ones in radically different ways. The AMBER94 does not distinguish terminal and
bridging atoms in carbohydrate chain. Carbon and hydrogen atoms correspond to the
CT and HC types.
At the same time, the OPLS distinguishes terminal and bridging atoms. Terminal
methyl groups correspond to type 10, while methylene groups correspond to type 9.
The OPLS has no aliphatic hydrogen atoms, which corresponds to the
united-atom model. Missing types are assigned to type 0.
Undefined parameters are marked by dash. In the above example, the charges on missing
types in the OPLS and all charges in AMBER94 are undefined. If charges are
undefined in the table, the values specified in the fields of atoms are used.
If they are undefined there too, zero values are used.
Using such tables, the program can associate atoms with types appropriate for a force field.
An initial association is made during the model construction, since the fragments, from
which the model is constructed, can be associated with a force field. This should be taken
into account so as not to build a discordant model from elements with different force fields.
The user can force the model to use the same force field
(Settings > Force field menu).
Note that force fields are defined only for some classes of substances and forcing a particular
force field has no effect for the molecules where this force field is unavailable. Finally,
even if all types are defined, the proper force field can be missing in the current version of
Unfortunately, force field association is a weak point in molecular mechanics modeling.
Development of a unique force field for the studied molecules can be the very desirably.
Currently, the program supports the molecular mechanics fields AMBER94 and OPLS as well as
fields for certain solvents (e.g., H2O, MeCN, DMSO, and CCl4).
Water is considered as a particular substance. The water force field can be retrieved from
the /bin/moldb/H2O.mmol file. By default, this file
describes the flexible SPC water model.
The force field data are stored in the /data/ForceField folder.
The file default.ff defines active force fields. The file with the
name of the current force field and ff extension includes the names of
files with the force field parameters. In addition, it specifies dielectric permittivity, 1–4
scaling factors for electrostatic and for van der Waals interactions, and the combinatorial rule
used to calculate parameters of van der Waals interactions between heterogeneous
atoms (arithmetic or geometric).
Let us exemplify an association of molecular mechanics types.
Open the Chain editor
press the –CHMe– button.
An isobutane molecule appears. Store it in the
press the –CH2– button. An isopentane molecule appears.
Store it in the
checking the types of atoms in these files shows that they are CT
and HC in one case or numeric values in
the other case. By default, the –CHMe– residue
is associated with the AMBER94 field; while adding the –CH2–
residue changes the association to the OPLS-AA field. This example shows that care should be taken
during model construction and the field in effect should be checked after each step;
change the association back to AMBER94 by selecting it in the
Settings > Force field menu. If the model is saved, we can check
that the atoms were assigned to the CT and HC
change the force field again by selecting OPLS in the Settings > Force field
menu. Note that all atoms are described by numeric values now. Moreover, carbon atoms are assigned to
different types! The OPLS distinguishes methyl groups depending to what they are attached to. That is why
the -CHMe- and –CH2–
groups have methyl stubs. These methyl groups belong to different
Fine types, which allows their correct conversion to OPLS types;
hydrogen atoms are assigned to type 0 in our model. This means that such atoms are missing
in the OPLS field. Hence, they can be removed from the model. Note that the removal of
hydrogen atoms is irreversible. It is recommended to save the model before this operation.
Selecting the Build > Strip menu item removes hydrogen atoms.