|
Miscellaneous Notes
- Do not remove the '======' separator lines.
- Units are in kcal/mol, Angstroms, degrees,
amu unless otherwise specified
- Sections can be in any order; i.e. BENDS can come before BONDS.
- All keywords are case sensitive and most are in ALL-CAPS
- Input is all free format
- Blank lines will be ignored
- 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 |
| ================ |
| 
