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The force field file is keyword driven with each key block defining parameters for each molecular mechanics interaction type such as bond types, angle types, torsion types, ...etc. The key block begins with the keyword, such as "BONDS".
The lines that actually contain the parameters are sandwiched between two lines that contain "========". The lines between the keyword and the first line containing "========" are not read by the program. These lines are intended for the user to define the columns as shown below. There can be as many lines between the keyword and the first '=====' as needed.
Example:
BONDS
Atoms pot K ro Notes
i - j type (kcal/molA^2) (Ang)
===================================
...
CA CA 1 938.0 1.400 amber95
CT CT 1 620.0 1.526 amber95
...
===================================
The force field atom types are the labels given to each atom in the real system that is used to generate the molecular mechanics portion of the QM/MM potential. These are separate from the atomic fragment types used by ADF for the electronic structure calculation. It is important to realize that QM atoms will have both an atomic fragment type and a force field atom type.
There are some limitations to the force field label types that the user can specify:
[Sigma] Labels can be a maximum of four characters long, with no spaces.
[Sigma] The atom types are case sensitive.
[Sigma] They can contain letters, numbers and other characters except ',' '.' or '=' and tabs.
Example of atom types that are not compatible with the program: C.3, C 3, C=3, C_sp3, *
Examples of atom types that are correct: C_3, C3, Csp3, and C*
Wild cards can be specified with the asterisk, `*'. Wild cards can be specified for angles, torsions and out-of-plane bends. Please refer to the specific sections for the limitations.
CAUTION: When using wild cards, place the wild cards at the beginning of the data section, beginning with the parameters with the most wild cards and ending with those that posses the least wild cards.
Example:
* C_3 * 100.310 111.000 two wild cards
* C_3 C_3 100.310 111.000 one wild card
C_2 C_3 C_3 100.310 111.000 no wild cards
If this ordering is not followed, then the wild card parameters will over-ride the specific parameters.
If the QM program uses dummy atoms, they are specified 'Xx' or 'XX'. The program will automatically remove dummy atoms from the non-bonded pair list. Please note that if the user specifics bonds to the dummy atom in the connection table, the program will look for the appropriate parameters in the force field file. The program does not filter out this possibility because sometimes it is useful to specify MM bonds to dummy atoms).
[Sigma] Do not remove the '======' separator lines.
[Sigma] Units are in kcal/mol, Angstroms, degrees, amu unless otherwise specified
[Sigma] Sections can be in any order; i.e. BENDS can come before BONDS.
[Sigma] All keywords are case sensitive and most are in ALL-CAPS
[Sigma] Input is all free format
[Sigma] Blank lines will be ignored
[Sigma] Comment lines can be added to parameter data sections by beginning the line with the '#' symbol.
Example:
H H 1.0080
HC H 1.0080
# example of comment line denoted with # mark.
H1 H 1.0080
H2 H 1.0080
4.3 A (partial) Example File
In this section we provide an example force field file to illustrate the format of the file. Only a limited number of parameters are included. A detailed description of each section of the force field file is provided in the next section.
FORCE_FIELD_SETTINGS
=================================
ELSTAT_1-4_SCALE 1.0000
VDW_1-4_SCALE 1.0000
VDW_DEFAULT_POTENTIAL 1 (1:6-12 2:exp-6 3:exp purely repulsive)
DIELECTRIC_CONSTANT 1.000
=================================
MASSES & ATOM LABELS
--------------------------------
force_field atomic
atom_type symbol mass NOTES
================================
C_3 C 12.0110 sp3 hybridized carbon
C_2 C 12.0110 sp2 hybridized carbon
C_1 C 12.0110 sp1 hybridized carbon
C_ar C 12.0110 aromatic
N_3 N 14.0070
N_2 N 14.0070
O_3 O 15.9990
================================
BONDS Ebond = 0.5*K(r-ro)**2
--------------------------------
Atoms pot
i - j type K R NOTES
================================
C_2 C_2 1 1340.00 1.335 WHITE_77
C_2 C_3 1 639.00 1.501 WHITE_75
C_3 C_3 1 633.60 1.540 *
C_3 N_2 1 760.20 1.440 *
================================
BENDS Ebend = 0.5*k(a-ao)^2
------------------------------------
Atoms pot
i - j - k type K theta NOTES
====================================
* C_2 * 1 78.79 120.00 WHITE_77
* C_3 * 1 65.66 109.50 WHITE_77
* C_ar * 1 78.79 120.00 *
C_ar C_2 N_2 1 131.31 120.00 *
C_3 C_3 C_ar 1 78.79 109.50 *
====================================
TORSIONS
-------------------------------------------
Atoms pot
i - j - k - l type k per NOTES
===========================================
* C_2 C_2 * 2 12.5000 -2.0
* C_1 C_3 * 2 0.0000 1.0
C_2 C_2 C_3 * 2 0.1260 -3.0
C_3 C_2 C_3 * 2 0.1260 3.0
H C_2 C_3 * 2 0.2740 3.0
* C_ar C_ar C_ar 2 2.3500 -2.0
* C_2 C_3 C_2 2 0.1260 3.0
* C_2 C_3 C_3 2 0.1260 3.0
C_3 C_3 C_3 C_3 0 0.5000 3.0 no torsion potential
C_2 C_2 C_3 C_2 2 0.1260 -3.0
C_3 C_3 N_2 C_2 1 0.5000 4 180.0 This and the next 3 lines
& 0.1500 3 180.0 are part of a multi-component
& 0.5300 1 0.0 Fourier potential
C_3 C_3 C_2 N_2 1 0.1000 4 0.0
& 0.0700 2 0.0 `&' is a continuation marker
===========================================
OUT-OF-PLANE
------------------------------
Atoms pot
i - j - k - l type K NOTES
==============================
* * C_2 * 2 480 TRIPOS_85
* * N_2 * 2 120 TRIPOS_85
H H N_2 C_3 2 120 TRIPOS_85
C_3 H N_2 * 2 120 TRIPOS_85
==============================
VAN DER WAALS
atom(s) Emin Rmin gamma NOTES
====================================
C_3 0.1070 3.4000 12.00
C_2 0.1070 3.4000 12.00
C_ca 0.1070 3.4000 12.00
C_ar 0.1070 3.4000 12.00
C_1 0.1070 3.4000 12.00
N_3 0.0950 3.1000 12.00
N_2 0.0950 3.1000 12.00
N_2 - N_2 2 0.0950 3.1000 12.00 purely repulsive potential for this pair
====================================
type charge(e) NOTES
=====================
OW -0.82 TIP3P water model
HW 0.41 TIP3P water model