The udff file: 1. File format¶
The udff file, or the user-define force field file, is a DL_FIELD input file where you can include new force field information that are not available in the library files.
A udff file allows you to define new FF models and parameters without tampering with the library files. You can also redefine the existing library data without doing any physical change to the library files.
The udff file structure
You can include DIRECTIVES from both the DL_FIELD’s sf and par library files. The general formats are shown as follows:
# General format of a udff file
POTENTIAL charmm22_prot
UNIT eV
[ATOM_TYPE]
..
..
[END ATOM_TYPE]
[MOLECULE_TYPE]
..
..
[END MOLECULE_TYPE]
[MOLECULE some_name]
..
..
[END MOLECULE]
[BOND]
..
..
[END BOND]
..
..
..
[VDW]
..
..
[END VDW]
END POTENTIAL
You can give any name to the file provided it ends with the extension .udff. Most DIRECTIVES are optional and a udff file can have as few as a single DIRECTIVE, perhaps to modify a set of parameters; or all DIRECTIVES, perhaps to fully define a complete FF model. In addition, the DIRECTIVES can also appear in any order according to your liking.
However, the following DIRECTIVES must always include in a udff file. For instance, the POTENTIAL and END POTENTIAL, within which the relevant FF data are located. In this case, the data is related to the CHARMM22_prot FF scheme. The way how data is displayed must also follow that of in the library files for that FF scheme.
The energy UNIT must also be specified within the POTENTIAL. DL_FIELD will assume all potential parameters will be expressed in this unit. In this example, all potential parameters would be expressed in the energy unit eV. Whereas, in the library, CHARMM22_prot FF is expressed in unit kcal/mol. DL_FIELD will carry out correct unit conversions, according to the energy unit specified in the DL_FIELD control file.
Note that more than one POTENTIAL scheme can be specified in a udff file, with the corresponding FF data enclosed within the appropriate POTENTIAL and END POTENTIAL directives. DL_FIELD will only look for the relevant data located within the appropriate POTENTIAL scheme according to the specification in the control file.
Using udff file
Once a udff file is constructed, DL_FIELD can read in the file by specifying the file in the control file as shown below, with the relevant rows being highlighted as follows:
Example control file.
1 * Construct DL_POLY output files
0 * NOT IN USE.
charmm22_prot * Type of force field require (see list below for choices).
kJ/mol * Energy unit: kcal/mol, kJ/mol, eV, or K.
normal * Conversion criteria (strict, normal, loose)
1 * Bond type (0=default, 1=harmonic , 2=Morse)
1 * Angle type (0=default, 1=harmonic, 2=harmonic cos)
/dl_f_4.8/workspace/example.udff * Include user-defined information. Put 'none' or a .udff filename
1 * Verbosity mode: 1 = on, 0 = off
Examples/sod1.pdb * Configuration file.
none * Output file in PDB. Put 'none' if not needed.
0 80 molecules 15.0 * Solution Maker: on/off, density, unit, cutoff)
...
...
In this control file, the udff file is specified. This means DL_FIELD will read this file before moving on to read the library files. DL_FIELD will only read in the information from the same FF scheme in the udff file.
In addition, the energy unit kJ/mol is specified. This means all the parameters will be automatically converted into this unit, whether they are from the udff or library sources.