| Cerius²·Forcefield Engines |
| Only the forcefield files for forcefields that were originally supplied with Cerius2 are documented in this section. |
This section shows the format of the forcefield parameter files used by Cerius2. They are ASCII files divided into 16 sections, each starting with a left-justified keyword and ending with the left-justified keyword END. This makes the parameter files easy to read; new sections can also be added easily.
Version number and product name
Keyword
VERSIONThe product name and the version number appear here. For example: CERIUS2 2
HEADERInformation for the user should be included here (such as forcefield and references). This is sent to standard output unchanged.
PREFERENCES
ATOMTYPES
| Variable | Format |
|---|---|
| atomtype,element,mass,charge,hyb,implhyds,lonepairs | (1X,A8,3X,A2,3X,F10.5,F8.4,3I4) |
DIAGONAL_VDW
ATOM_TYPING_RULES
| Variable | Format |
|---|---|
| atomtype,element,hyb,ring,shell,factor | (1X,A5,3X,8X,A2,4I12) |
OFF_DIAGONAL_VDW
BOND_STRETCH
ANGLE_BEND
TORSIONS
| Variable | Format |
|---|---|
| ffi,ffj,ffk,ffl,'DIHEDRAL ',kw,n,w0 | (1X,3(A5,4X),A5,3X,4X,A10,1X,3F10.4) |
| ffi,ffj,ffk,ffl,'IGNORE ' | (1X,3(A5,4X),A5,3X,4X,A10) |
INVERSIONS
UREY_BRADLEY
| Variable | Format |
|---|---|
| ffi,ffj,ffk,'HARMONIC ',kub,r0,d | (1X,A5,4X,A5,4X,A5,3X,4X,A10,1X,3F10.4) |
| ffi,ffj,ffk,'IGNORE ' | (1X,A5,4X,A5,4X,A5,3X,4X,A10) |
HYDROGEN_BONDS
| Variable | Format |
|---|---|
| ffi,ffj,'MORSE ',de,re,y | (1X,A5,4X,A5,3X,4X,A10,1X,E12.4,2F10.4) |
| ffi,ffj,'LJ_12_10 ',de,re | (1X,A5,4X,A5,3X,4X,A10,1X,E12.4,1F10.4) |
| ffi,ffj,'IGNORE ' | (1X,A5,4X,A5,3X,4X,A10) |
GENERATOR
| Variable | Format |
|---|---|
| ffi, aradius, aangle, azstar, azeta, auenerg, auang, iaprd, iacis, atorbar, ElectNeg | (1X,A5,3X,2X,6F10.4,2I10,F10.4,F10.5) |
STRETCH_BEND_STRETCH
STRETCH_STRETCH
| Variable | Format |
|---|---|
| ffi,ffj,ffk,'SIMPLE ',r01,r02,k12 | (1X,A5,4X,A5,4X,A5,3X,4X,A10,1X,3F10.4) |
Because forcefield parameter files produced by CERIUS or POLYGRAF cannot be read by Cerius2, all CERIUS forcefield parameter files and the Dreiding321 of POLYGRAF have been converted into the new Cerius2 format. These forcefields are available within the Cerius2-Resources/FORCE-FIELD directory and its subdirectories (see 1, "Using the Open Force Field").
Pf forcefield parameter file converter
> pf [-CI or -G] IN_ff_parameter_file OUT_ff_parameter_fileThe optional arguments specify if the origin of the input file is CERIUS (-CI) or POLYGRAF (-G) and are a safeguard in case the converter cannot decipher the source of the parameter file.
For example, to convert a CERIUS forcefield file named myoldforcefield.par to a Cerius2 forcefield file named mynewforce-field1.01, type:
> pf -CI myoldforcefield.par mynewforcefield1.01If the energies obtained with the converted forcefield are different from those obtained with the original forcefield, then carefully examine the cross terms and options described below.
Options
During conversion of a POLYGRAF forcefield parameter file you may notice a number of warning messages reported to the text window. This is because some options are not yet supported, or their underlying actions may be treated in a different way by Cerius2 than by POLYGRAF. When such an option is found by the converter, the parameter file section for that option is skipped.
During file conversion the following warning may appear in the text window:
WARNING: Some atom types masses read in differ from their expected mass. The expected mass is given by the element mass + Number of implicit hydrogens. Therefore some masses have been adjusted.This happens when an atom type with implicit hydrogens is found during conversion. In this case, the converter first determines whether the masses of the implicit hydrogens have already been added to the atom's mass and, if not, it adds them.
twist terms.