Molecular mechanics Force Field association
The association of appropriate molecular mechanics types with atoms is a process that difficult to automate. 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.
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 Fine 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 the program.
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 force fields AMBER 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 default force field on the program start. 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).