atom number | atom name | GROMOS atom type | el. charge | charge group |
1 | FELJ | FELJ | 1.00000 | 1 |
2 | NA | NP | -0.40000 | 1 |
3 | NB | NP | -0.40000 | 1 |
4 | NC | NP | -0.40000 | 1 |
5 | ND | NP | -0.40000 | 1 |
6 | CHA | CR61 | 0.10000 | 2 |
7 | C1A | CB | 0.00000 | 3 |
8 | C2A | CB | 0.00000 | 4 |
9 | C3A | CB | 0.00000 | 5 |
10 | C4A | CB | 0.00000 | 6 |
11 | CMA | CH3 | 0.20000 | 7 |
12 | CAA | CH2 | 0.00000 | 8 |
13 | CBA | CH2 | 0.00000 | 9 |
14 | CGA | C | 0.27000 | 10 |
15 | O1A | OM | -0.63500 | 10 |
16 | O2A | OM | -0.63500 | 10 |
17 | CHB | CR61 | 0.10000 | 11 |
18 | C1B | CB | 0.00000 | 12 |
19 | C2B | CB | 0.00000 | 13 |
20 | C3B | CB | 0.00000 | 14 |
21 | C4B | CB | 0.00000 | 15 |
22 | CMB | CH3 | 0.20000 | 16 |
23 | CAB | CR61 | 0.00000 | 17 |
24 | CBB | CH2 | 0.00000 | 18 |
25 | CHC | CR61 | 0.10000 | 19 |
26 | C1C | CB | 0.00000 | 20 |
27 | C2C | CB | 0.00000 | 21 |
28 | C3C | CB | 0.00000 | 22 |
29 | C4C | CB | 0.00000 | 23 |
30 | CMC | CH3 | 0.20000 | 24 |
31 | CAC | CR61 | 0.00000 | 25 |
32 | CBC | CH2 | 0.00000 | 26 |
33 | CHD | CR61 | 0.10000 | 27 |
34 | C1D | CB | 0.00000 | 28 |
35 | C2D | CB | 0.00000 | 29 |
36 | C3D | CB | 0.00000 | 30 |
37 | C4D | CB | 0.00000 | 31 |
38 | CMD | CH3 | 0.20000 | 32 |
39 | CAD | CH2 | 0.00000 | 33 |
40 | CBD | CH2 | 0.00000 | 34 |
41 | CGD | C | 0.27000 | 35 |
42 | O1D | OM | -0.63500 | 35 |
43 | O2D | OM | -0.63500 | 35 |
bond number | atom i | atom j | if 0:standard GROMOS parameters, if 1: new parameters | (ignore) | bond length [nm] | force constant [kJ/nm**2/mol] |
1 | 1 | 2 | 1 | 0 | 0.20900 | 4.18400E+05 |
2 | 1 | 3 | 1 | 0 | 0.20900 | 4.18400E+05 |
3 | 1 | 4 | 1 | 0 | 0.20900 | 4.18400E+05 |
4 | 1 | 5 | 1 | 0 | 0.20900 | 4.18400E+05 |
5 | 2 | 7 | 0 | 0 | ||
6 | 2 | 10 | 0 | 0 | ||
7 | 3 | 18 | 0 | 0 | ||
8 | 3 | 21 | 0 | 0 | ||
9 | 4 | 26 | 0 | 0 | ||
10 | 4 | 29 | 0 | 0 | ||
11 | 5 | 34 | 0 | 0 | ||
12 | 5 | 37 | 0 | 0 | ||
13 | 6 | 37 | 0 | 0 | ||
14 | 6 | 7 | 0 | 0 | ||
15 | 7 | 8 | 0 | 0 | ||
16 | 8 | 9 | 0 | 0 | ||
17 | 8 | 12 | 0 | 0 | ||
18 | 9 | 10 | 0 | 0 | ||
19 | 9 | 11 | 0 | 0 | ||
20 | 10 | 17 | 0 | 0 | ||
21 | 12 | 13 | 0 | 0 | ||
22 | 13 | 14 | 0 | 0 | ||
23 | 14 | 15 | 0 | 0 | ||
24 | 14 | 16 | 0 | 0 | ||
25 | 17 | 18 | 0 | 0 | ||
26 | 18 | 19 | 0 | 0 | ||
27 | 19 | 20 | 0 | 0 | ||
28 | 19 | 22 | 0 | 0 | ||
29 | 20 | 21 | 0 | 0 | ||
30 | 20 | 23 | 1 | 0 | 0.15300 | 3.34720E+05 |
31 | 21 | 25 | 0 | 0 | ||
32 | 23 | 24 | 0 | 0 | ||
33 | 25 | 26 | 0 | 0 | ||
34 | 26 | 27 | 0 | 0 | ||
35 | 27 | 28 | 0 | 0 | ||
36 | 27 | 30 | 0 | 0 | ||
37 | 28 | 29 | 0 | 0 | ||
38 | 28 | 31 | 1 | 0 | 0.15300 | 3.34720E+05 |
39 | 29 | 33 | 0 | 0 | ||
40 | 31 | 32 | 0 | 0 | ||
41 | 33 | 34 | 0 | 0 | ||
42 | 34 | 35 | 0 | 0 | ||
43 | 35 | 36 | 0 | 0 | ||
44 | 35 | 38 | 0 | 0 | ||
45 | 36 | 37 | 0 | 0 | ||
46 | 36 | 39 | 0 | 0 | ||
47 | 39 | 40 | 0 | 0 | ||
48 | 40 | 41 | 0 | 0 | ||
49 | 41 | 42 | 0 | 0 | ||
50 | 41 | 43 | 0 | 0 | ||
51 | -21 | 1 | 1 | 0 | 0.22000 | 4.18400E+05 |
bond angle number | atom i | atom j | atom k | if 0:standard GROMOS parameters, if 1: new parameters | (ignore) | bond angle [rad] | force constant [kJ/rad**2/mol] |
1 | 2 | 1 | 3 | 1 | 0 | 1.57080 | 0.41840E+03 |
2 | 3 | 1 | 4 | 1 | 0 | 1.57080 | 0.41840E+03 |
3 | 4 | 1 | 5 | 1 | 0 | 1.57080 | 0.41840E+03 |
4 | 2 | 1 | 5 | 1 | 0 | 1.57080 | 0.41840E+03 |
5 | 2 | 1 | 4 | 1 | 0 | 2.71556 | 0.41840E+03 |
6 | 3 | 1 | 5 | 1 | 0 | 2.71556 | 0.41840E+03 |
7 | 1 | 2 | 7 | 1 | 0 | 2.19911 | 0.41840E+03 |
8 | 1 | 2 | 10 | 1 | 0 | 2.19911 | 0.41840E+03 |
9 | 7 | 2 | 10 | 1 | 0 | 1.88496 | 0.37656E+03 |
10 | 1 | 3 | 18 | 1 | 0 | 2.19911 | 0.41840E+03 |
11 | 1 | 3 | 21 | 1 | 0 | 2.19911 | 0.41840E+03 |
12 | 18 | 3 | 21 | 1 | 0 | 1.88496 | 0.37656E+03 |
13 | 1 | 4 | 26 | 1 | 0 | 2.19911 | 0.41840E+03 |
14 | 1 | 4 | 29 | 1 | 0 | 2.19911 | 0.41840E+03 |
15 | 26 | 4 | 29 | 1 | 0 | 1.88496 | 0.37656E+03 |
16 | 1 | 5 | 34 | 1 | 0 | 2.19911 | 0.41840E+03 |
17 | 1 | 5 | 37 | 1 | 0 | 2.19911 | 0.41840E+03 |
18 | 34 | 5 | 37 | 1 | 0 | 1.88496 | 0.37656E+03 |
19 | 7 | 6 | 37 | 1 | 0 | 2.19911 | 0.41840E+03 |
20 | 2 | 7 | 8 | 1 | 0 | 1.88496 | 0.41840E+03 |
21 | 6 | 7 | 8 | 1 | 0 | 2.19911 | 0.41840E+03 |
22 | 2 | 7 | 6 | 1 | 0 | 2.19911 | 0.41840E+03 |
23 | 7 | 8 | 12 | 1 | 0 | 2.19911 | 0.41840E+03 |
24 | 9 | 8 | 12 | 1 | 0 | 2.19911 | 0.41840E+03 |
25 | 7 | 8 | 9 | 1 | 0 | 1.88496 | 0.41840E+03 |
26 | 8 | 9 | 11 | 1 | 0 | 2.19911 | 0.41840E+03 |
27 | 10 | 9 | 11 | 1 | 0 | 2.19911 | 0.41840E+03 |
28 | 8 | 9 | 10 | 1 | 0 | 1.88496 | 0.41840E+03 |
29 | 2 | 10 | 17 | 1 | 0 | 2.19911 | 0.41840E+03 |
30 | 9 | 10 | 17 | 1 | 0 | 2.19911 | 0.41840E+03 |
31 | 2 | 10 | 9 | 1 | 0 | 1.88496 | 0.41840E+03 |
32 | 8 | 12 | 13 | 1 | 0 | 1.93732 | 0.46024E+03 |
33 | 12 | 13 | 14 | 1 | 0 | 1.93732 | 0.46024E+03 |
34 | 13 | 14 | 16 | 1 | 0 | 2.04204 | 0.50208E+03 |
35 | 15 | 14 | 16 | 1 | 0 | 2.19911 | 0.50208E+03 |
36 | 13 | 14 | 15 | 1 | 0 | 2.04204 | 0.50208E+03 |
37 | 10 | 17 | 18 | 1 | 0 | 2.19911 | 0.41840E+03 |
38 | 3 | 18 | 17 | 1 | 0 | 2.19911 | 0.41840E+03 |
39 | 17 | 18 | 19 | 1 | 0 | 2.19911 | 0.41840E+03 |
40 | 3 | 18 | 19 | 1 | 0 | 1.88496 | 0.41840E+03 |
41 | 18 | 19 | 22 | 1 | 0 | 2.19911 | 0.41840E+03 |
42 | 20 | 19 | 22 | 1 | 0 | 2.19911 | 0.41840E+03 |
43 | 18 | 19 | 20 | 1 | 0 | 1.88496 | 0.41840E+03 |
44 | 19 | 20 | 23 | 1 | 0 | 2.19911 | 0.41840E+03 |
45 | 21 | 20 | 23 | 1 | 0 | 2.19911 | 0.41840E+03 |
46 | 19 | 20 | 21 | 1 | 0 | 1.88496 | 0.41840E+03 |
47 | 3 | 21 | 25 | 1 | 0 | 2.19911 | 0.41840E+03 |
48 | 20 | 21 | 25 | 1 | 0 | 2.19911 | 0.41840E+03 |
49 | 3 | 21 | 20 | 1 | 0 | 1.88496 | 0.41840E+03 |
50 | 20 | 23 | 24 | 1 | 0 | 2.19911 | 0.41840E+03 |
51 | 21 | 25 | 26 | 1 | 0 | 2.19911 | 0.41840E+03 |
52 | 4 | 26 | 25 | 1 | 0 | 2.19911 | 0.41840E+03 |
53 | 25 | 26 | 27 | 1 | 0 | 2.19911 | 0.41840E+03 |
54 | 4 | 26 | 27 | 1 | 0 | 1.88496 | 0.41840E+03 |
55 | 26 | 27 | 30 | 1 | 0 | 2.19911 | 0.41840E+03 |
56 | 28 | 27 | 30 | 1 | 0 | 2.19911 | 0.41840E+03 |
57 | 26 | 27 | 28 | 1 | 0 | 1.88496 | 0.41840E+03 |
58 | 27 | 28 | 31 | 1 | 0 | 2.19911 | 0.41840E+03 |
59 | 29 | 28 | 31 | 1 | 0 | 2.19911 | 0.41840E+03 |
60 | 27 | 28 | 29 | 1 | 0 | 1.88496 | 0.41840E+03 |
61 | 4 | 29 | 33 | 1 | 0 | 2.19911 | 0.41840E+03 |
62 | 28 | 29 | 33 | 1 | 0 | 2.19911 | 0.41840E+03 |
63 | 4 | 29 | 28 | 1 | 0 | 1.88496 | 0.41840E+03 |
64 | 28 | 31 | 32 | 1 | 0 | 2.19911 | 0.41840E+03 |
65 | 29 | 33 | 34 | 1 | 0 | 2.19911 | 0.41840E+03 |
66 | 5 | 34 | 33 | 1 | 0 | 2.19911 | 0.41840E+03 |
67 | 33 | 34 | 35 | 1 | 0 | 2.19911 | 0.41840E+03 |
68 | 5 | 34 | 35 | 1 | 0 | 1.88496 | 0.41840E+03 |
69 | 34 | 35 | 38 | 1 | 0 | 2.19911 | 0.41840E+03 |
70 | 36 | 35 | 38 | 1 | 0 | 2.19911 | 0.41840E+03 |
71 | 34 | 35 | 36 | 1 | 0 | 1.88496 | 0.41840E+03 |
72 | 35 | 36 | 39 | 1 | 0 | 2.19911 | 0.41840E+03 |
73 | 37 | 36 | 39 | 1 | 0 | 2.19911 | 0.41840E+03 |
74 | 35 | 36 | 37 | 1 | 0 | 1.88496 | 0.41840E+03 |
75 | 5 | 37 | 6 | 1 | 0 | 2.19911 | 0.41840E+03 |
76 | 6 | 37 | 36 | 1 | 0 | 2.19911 | 0.41840E+03 |
77 | 5 | 37 | 36 | 1 | 0 | 1.88496 | 0.41840E+03 |
78 | 36 | 39 | 40 | 1 | 0 | 1.93732 | 0.46024E+03 |
79 | 39 | 40 | 41 | 1 | 0 | 1.93732 | 0.46024E+03 |
80 | 40 | 41 | 43 | 1 | 0 | 2.04204 | 0.50208E+03 |
81 | 42 | 41 | 43 | 1 | 0 | 2.19911 | 0.50208E+03 |
82 | 40 | 41 | 42 | 1 | 0 | 2.04204 | 0.50208E+03 |
83 | -21 | 1 | 2 | 1 | 0 | 1.78024 | 0.41840E+03 |
84 | -21 | 1 | 3 | 1 | 0 | 1.78024 | 0.41840E+03 |
85 | -21 | 1 | 4 | 1 | 0 | 1.78024 | 0.41840E+03 |
86 | -21 | 1 | 5 | 1 | 0 | 1.78024 | 0.41840E+03 |
87 | -22 | -21 | 1 | 1 | 0 | 1.91114 | 0.25104E+03 |
torsion number | atom i | atom j | atom k | atom l | if 0:standard GROMOS parameters, if 1: new parameters | (ignore) | torsion [rad] | force constant [kJ/rad**2/mol] | periodicity |
1 | 2 | 10 | 17 | 18 | 0 | 0 | |||
2 | 10 | 17 | 18 | 3 | 0 | 0 | |||
3 | 3 | 21 | 25 | 26 | 0 | 0 | |||
4 | 21 | 25 | 26 | 4 | 0 | 0 | |||
5 | 4 | 29 | 33 | 34 | 0 | 0 | |||
6 | 29 | 33 | 34 | 5 | 0 | 0 | |||
7 | 5 | 37 | 6 | 7 | 0 | 0 | |||
8 | 37 | 6 | 7 | 2 | 0 | 0 | |||
9 | 7 | 8 | 12 | 13 | 0 | 0 | |||
10 | 8 | 12 | 13 | 14 | 0 | 0 | |||
11 | 12 | 13 | 14 | 15 | 0 | 0 | |||
12 | 19 | 20 | 23 | 24 | 1 | 0 | 0.00000 | 4.18400E-01 | 2 |
13 | 27 | 28 | 31 | 32 | 1 | 0 | 0.00000 | 4.18400E-01 | 2 |
14 | 35 | 36 | 39 | 40 | 0 | 0 | |||
15 | 36 | 39 | 40 | 41 | 0 | 0 | |||
16 | 39 | 40 | 41 | 42 | 0 | 0 | |||
17 | -22 | -21 | 1 | 2 | 1 | 0 | 0.00000 | 0.00000E+00 | 4 |
improper torsion number | atom i | atom j | atom k | atom l | if 0:standard GROMOS parameters, if 1: new parameters | (ignore) | torsion [rad] | force constant [kJ/rad**2/mol] |
1 | 1 | 7 | 10 | 2 | 1 | 0 | 0.15053 | 1.67360E+02 |
2 | 1 | 18 | 21 | 3 | 1 | 0 | 0.15053 | 1.67360E+02 |
3 | 1 | 26 | 29 | 4 | 1 | 0 | 0.15053 | 1.67360E+02 |
4 | 1 | 34 | 37 | 5 | 1 | 0 | 0.15053 | 1.67360E+02 |
5 | 7 | 2 | 8 | 6 | 0 | 0 | ||
6 | 10 | 9 | 2 | 17 | 0 | 0 | ||
7 | 18 | 19 | 3 | 17 | 0 | 0 | ||
8 | 21 | 3 | 25 | 20 | 0 | 0 | ||
9 | 26 | 4 | 27 | 25 | 0 | 0 | ||
10 | 29 | 28 | 4 | 33 | 0 | 0 | ||
11 | 34 | 5 | 35 | 33 | 0 | 0 | ||
12 | 37 | 36 | 5 | 6 | 0 | 0 | ||
13 | 8 | 7 | 9 | 12 | 0 | 0 | ||
14 | 9 | 8 | 10 | 11 | 0 | 0 | ||
15 | 19 | 18 | 20 | 22 | 0 | 0 | ||
16 | 20 | 19 | 21 | 23 | 0 | 0 | ||
17 | 27 | 26 | 28 | 30 | 0 | 0 | ||
18 | 28 | 27 | 29 | 31 | 0 | 0 | ||
19 | 35 | 34 | 36 | 38 | 0 | 0 | ||
20 | 36 | 35 | 37 | 39 | 0 | 0 | ||
21 | 13 | 15 | 16 | 14 | 0 | 0 | ||
22 | 40 | 42 | 43 | 41 | 0 | 0 | ||
23 | 21 | 18 | 19 | 23 | 0 | 0 | ||
24 | 19 | 3 | 21 | 23 | 0 | 0 | ||
25 | 19 | 21 | 18 | 23 | 0 | 0 | ||
26 | 29 | 26 | 27 | 31 | 0 | 0 | ||
27 | 27 | 4 | 29 | 31 | 0 | 0 | ||
28 | 27 | 29 | 26 | 31 | 0 | 0 | ||
29 | 7 | 9 | 8 | 10 | 0 | 0 | ||
30 | 8 | 10 | 9 | 2 | 0 | 0 | ||
31 | 7 | 10 | 8 | 2 | 0 | 0 | ||
32 | 18 | 20 | 19 | 21 | 0 | 0 | ||
33 | 19 | 21 | 20 | 3 | 0 | 0 | ||
34 | 18 | 21 | 19 | 3 | 0 | 0 | ||
35 | 26 | 28 | 27 | 29 | 0 | 0 | ||
36 | 27 | 29 | 28 | 4 | 0 | 0 | ||
37 | 26 | 29 | 27 | 4 | 0 | 0 | ||
38 | 34 | 36 | 35 | 37 | 0 | 0 | ||
39 | 35 | 37 | 36 | 5 | 0 | 0 | ||
40 | 34 | 37 | 35 | 5 | 0 | 0 | ||
41 | 10 | 18 | 17 | 2 | 0 | 0 | ||
42 | 18 | 10 | 17 | 3 | 0 | 0 | ||
43 | 21 | 26 | 25 | 3 | 0 | 0 | ||
44 | 26 | 21 | 25 | 4 | 0 | 0 | ||
45 | 29 | 34 | 33 | 4 | 0 | 0 | ||
46 | 34 | 29 | 33 | 5 | 0 | 0 | ||
47 | 37 | 7 | 6 | 5 | 0 | 0 | ||
48 | 7 | 37 | 6 | 2 | 0 | 0 | ||
49 | 19 | 21 | 3 | 23 | 0 | 0 | ||
50 | 27 | 29 | 4 | 31 | 0 | 0 | ||
51 | 7 | 9 | 2 | 12 | 0 | 0 | ||
52 | 7 | 9 | 10 | 12 | 0 | 0 | ||
53 | 35 | 37 | 34 | 39 | 0 | 0 | ||
54 | 35 | 37 | 5 | 39 | 0 | 0 |
atom number | atom name | GROMOS atom type | el. charge | charge group |
1 | N | N | -0.28000 | 1 |
2 | H | H | 0.28000 | 1 |
3 | CA | CH1 | 0.00000 | 2 |
4 | CB | CH2 | -0.10000 | 3 |
5 | SG | S | -0.50000 | 4 |
6 | C | C | 0.38000 | 5 |
7 | O | O | -0.38000 | 5 |
[2] Harris & Loew, JACS, 115, 8775 (1993)
[3] Jones et al., JACS, 115, 382 (1993)
[4] V.Helms & R.C.Wade Thermodynamics of Water Mediating Protein-Ligand Interactions in Cytochrome P450cam: A Molecular Dynamics Study Biophys. J. (1995) 69, 810-824.
Last Updated: April 27, 2000 3:34 pm