Files::STOP
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A STOP file is a simplified topology. The easiest way how to generate this file is to use the top2stop command.
Example
[atom_types]
! Index Type Mass Z
1 c3 12.0100 6
2 hc 1.0080 1
[atoms]
! Index Type Name ResID ResN Charge Type
1 1 C1 1 BUT -0.092499 ! c3
2 2 H11 1 BUT 0.018863 ! hc
3 2 H12 1 BUT 0.018863 ! hc
4 2 H13 1 BUT 0.018863 ! hc
5 1 C2 1 BUT 0.030891 ! c3
6 2 H21 1 BUT 0.002509 ! hc
7 2 H22 1 BUT 0.002509 ! hc
8 1 C3 1 BUT 0.030891 ! c3
9 2 H31 1 BUT 0.002509 ! hc
10 2 H32 1 BUT 0.002509 ! hc
11 1 C4 1 BUT -0.092499 ! c3
12 2 H41 1 BUT 0.018863 ! hc
13 2 H42 1 BUT 0.018863 ! hc
14 2 H43 1 BUT 0.018863 ! hc
[bond_types]
! 0.5*k(d-d0)^2
! Index TypeA TypeB Form d0 K TypeA TypeB
1 1 2 1 1.097000 751.840000 ! c3 hc
2 1 1 1 1.538000 465.040000 ! c3 c3
[bonds]
! Index AtomA AtomB Type AtomA TypeA AtomB TypeB
1 1 5 2 ! C1 c3 C2 c3
2 5 8 2 ! C2 c3 C3 c3
3 8 11 2 ! C3 c3 C4 c3
4 1 4 1 ! C1 c3 H13 hc
5 1 3 1 ! C1 c3 H12 hc
6 1 2 1 ! C1 c3 H11 hc
7 5 7 1 ! C2 c3 H22 hc
8 5 6 1 ! C2 c3 H21 hc
9 8 10 1 ! C3 c3 H32 hc
10 8 9 1 ! C3 c3 H31 hc
11 11 14 1 ! C4 c3 H43 hc
12 11 13 1 ! C4 c3 H42 hc
13 11 12 1 ! C4 c3 H41 hc
[angle_types]
! 0.5*k(a-a0)^2
! Index TypeA TypeB TypeC Form a0 K TypeA TypeB TypeC
1 1 1 2 1 1.916372 93.632000 ! c3 c3 hc
2 1 1 1 1 1.946217 129.776000 ! c3 c3 c3
3 2 1 2 1 1.877626 77.920000 ! hc c3 hc
[angles]
! Index AtomA AtomB AtomC Type AtomA TypeA AtomB TypeB AtomC TypeC
1 1 5 8 2 ! C1 c3 C2 c3 C3 c3
2 5 8 11 2 ! C2 c3 C3 c3 C4 c3
3 1 5 7 1 ! C1 c3 C2 c3 H22 hc
4 1 5 6 1 ! C1 c3 C2 c3 H21 hc
5 2 1 4 3 ! H11 hc C1 c3 H13 hc
6 2 1 3 3 ! H11 hc C1 c3 H12 hc
7 2 1 5 1 ! H11 hc C1 c3 C2 c3
8 3 1 4 3 ! H12 hc C1 c3 H13 hc
9 3 1 5 1 ! H12 hc C1 c3 C2 c3
10 4 1 5 1 ! H13 hc C1 c3 C2 c3
11 5 8 10 1 ! C2 c3 C3 c3 H32 hc
12 5 8 9 1 ! C2 c3 C3 c3 H31 hc
13 6 5 7 3 ! H21 hc C2 c3 H22 hc
14 6 5 8 1 ! H21 hc C2 c3 C3 c3
15 7 5 8 1 ! H22 hc C2 c3 C3 c3
16 8 11 14 1 ! C3 c3 C4 c3 H43 hc
17 8 11 13 1 ! C3 c3 C4 c3 H42 hc
18 8 11 12 1 ! C3 c3 C4 c3 H41 hc
19 9 8 10 3 ! H31 hc C3 c3 H32 hc
20 9 8 11 1 ! H31 hc C3 c3 C4 c3
21 10 8 11 1 ! H32 hc C3 c3 C4 c3
22 12 11 14 3 ! H41 hc C4 c3 H43 hc
23 12 11 13 3 ! H41 hc C4 c3 H42 hc
24 13 11 14 3 ! H42 hc C4 c3 H43 hc
[dihedral_types]
! Index TypeA TypeB TypeC TypeD Form scee scnb TypeA TypeB TypeC TypeD
1 1 1 1 1 1 1.200000 2.000000 ! c3 c3 c3 c3
2 1 1 1 2 1 1.200000 2.000000 ! c3 c3 c3 hc
3 2 1 1 2 1 1.200000 2.000000 ! hc c3 c3 hc
[dihedral_seq_cos]
! Type pn v0 phase
1 1 0.110000 0.000000
1 2 0.290000 3.141594
1 3 0.130000 0.000000
1 4 0.000000 0.000000
2 1 0.000000 0.000000
2 2 0.000000 0.000000
2 3 0.080000 0.000000
2 4 0.000000 0.000000
3 1 0.000000 0.000000
3 2 0.000000 0.000000
3 3 0.120000 0.000000
3 4 0.000000 0.000000
[dihedrals]
! Index AtomA AtomB AtomC AtomD Type AtomA TypeA AtomB TypeB AtomC TypeC AtomD TypeD
1 1 5 8 11 1 ! C1 c3 C2 c3 C3 c3 C4 c3
2 1 5 8 10 2 ! C1 c3 C2 c3 C3 c3 H32 hc
3 1 5 8 9 2 ! C1 c3 C2 c3 C3 c3 H31 hc
4 2 1 5 7 3 ! H11 hc C1 c3 C2 c3 H22 hc
5 2 1 5 6 3 ! H11 hc C1 c3 C2 c3 H21 hc
6 2 1 5 8 2 ! H11 hc C1 c3 C2 c3 C3 c3
7 3 1 5 7 3 ! H12 hc C1 c3 C2 c3 H22 hc
8 3 1 5 6 3 ! H12 hc C1 c3 C2 c3 H21 hc
9 3 1 5 8 2 ! H12 hc C1 c3 C2 c3 C3 c3
10 4 1 5 7 3 ! H13 hc C1 c3 C2 c3 H22 hc
11 4 1 5 6 3 ! H13 hc C1 c3 C2 c3 H21 hc
12 4 1 5 8 2 ! H13 hc C1 c3 C2 c3 C3 c3
13 5 8 11 14 2 ! C2 c3 C3 c3 C4 c3 H43 hc
14 5 8 11 13 2 ! C2 c3 C3 c3 C4 c3 H42 hc
15 5 8 11 12 2 ! C2 c3 C3 c3 C4 c3 H41 hc
16 6 5 8 10 3 ! H21 hc C2 c3 C3 c3 H32 hc
17 6 5 8 9 3 ! H21 hc C2 c3 C3 c3 H31 hc
18 6 5 8 11 2 ! H21 hc C2 c3 C3 c3 C4 c3
19 7 5 8 10 3 ! H22 hc C2 c3 C3 c3 H32 hc
20 7 5 8 9 3 ! H22 hc C2 c3 C3 c3 H31 hc
21 7 5 8 11 2 ! H22 hc C2 c3 C3 c3 C4 c3
22 9 8 11 14 3 ! H31 hc C3 c3 C4 c3 H43 hc
23 9 8 11 13 3 ! H31 hc C3 c3 C4 c3 H42 hc
24 9 8 11 12 3 ! H31 hc C3 c3 C4 c3 H41 hc
25 10 8 11 14 3 ! H32 hc C3 c3 C4 c3 H43 hc
26 10 8 11 13 3 ! H32 hc C3 c3 C4 c3 H42 hc
27 10 8 11 12 3 ! H32 hc C3 c3 C4 c3 H41 hc
[improper_types]
! Index TypeA TypeB TypeC TypeD v0 phase TypeA TypeB TypeC TypeD
[impropers]
! Index AtomA AtomB AtomC AtomD Type AtomA TypeA AtomB TypeB AtomC TypeC AtomD TypeD
[nb_types]
! Index TypA TypB eps r0 alpha ! TypeA TypeB
1 1 1 0.1078000 3.8138000 0.0000000 ! c3 c3
2 1 2 0.0473523 3.3662000 0.0000000 ! c3 hc
3 2 2 0.0208000 2.9186000 0.0000000 ! hc hc
[nb_list]
! Index AtomA AtomB Type Dihed AtomA TypeA AtomB TypeB
1 1 9 2 2 ! C1 c3 H31 hc
2 1 10 2 2 ! C1 c3 H32 hc
3 1 11 1 1 ! C1 c3 C4 c3
4 1 12 2 0 ! C1 c3 H41 hc
5 1 13 2 0 ! C1 c3 H42 hc
6 1 14 2 0 ! C1 c3 H43 hc
7 2 6 3 3 ! H11 hc H21 hc
8 2 7 3 3 ! H11 hc H22 hc
9 2 8 2 2 ! H11 hc C3 c3
10 2 9 3 0 ! H11 hc H31 hc
11 2 10 3 0 ! H11 hc H32 hc
12 2 11 2 0 ! H11 hc C4 c3
13 2 12 3 0 ! H11 hc H41 hc
14 2 13 3 0 ! H11 hc H42 hc
15 2 14 3 0 ! H11 hc H43 hc
16 3 6 3 3 ! H12 hc H21 hc
17 3 7 3 3 ! H12 hc H22 hc
18 3 8 2 2 ! H12 hc C3 c3
19 3 9 3 0 ! H12 hc H31 hc
20 3 10 3 0 ! H12 hc H32 hc
21 3 11 2 0 ! H12 hc C4 c3
22 3 12 3 0 ! H12 hc H41 hc
23 3 13 3 0 ! H12 hc H42 hc
24 3 14 3 0 ! H12 hc H43 hc
25 4 6 3 3 ! H13 hc H21 hc
26 4 7 3 3 ! H13 hc H22 hc
27 4 8 2 2 ! H13 hc C3 c3
28 4 9 3 0 ! H13 hc H31 hc
29 4 10 3 0 ! H13 hc H32 hc
30 4 11 2 0 ! H13 hc C4 c3
31 4 12 3 0 ! H13 hc H41 hc
32 4 13 3 0 ! H13 hc H42 hc
33 4 14 3 0 ! H13 hc H43 hc
34 5 12 2 2 ! C2 c3 H41 hc
35 5 13 2 2 ! C2 c3 H42 hc
36 5 14 2 2 ! C2 c3 H43 hc
37 6 9 3 3 ! H21 hc H31 hc
38 6 10 3 3 ! H21 hc H32 hc
39 6 11 2 2 ! H21 hc C4 c3
40 6 12 3 0 ! H21 hc H41 hc
41 6 13 3 0 ! H21 hc H42 hc
42 6 14 3 0 ! H21 hc H43 hc
43 7 9 3 3 ! H22 hc H31 hc
44 7 10 3 3 ! H22 hc H32 hc
45 7 11 2 2 ! H22 hc C4 c3
46 7 12 3 0 ! H22 hc H41 hc
47 7 13 3 0 ! H22 hc H42 hc
48 7 14 3 0 ! H22 hc H43 hc
49 9 12 3 3 ! H31 hc H41 hc
50 9 13 3 3 ! H31 hc H42 hc
51 9 14 3 3 ! H31 hc H43 hc
52 10 12 3 3 ! H32 hc H41 hc
53 10 13 3 3 ! H32 hc H42 hc
54 10 14 3 3 ! H32 hc H43 hc
[dimensions]
! Scope Size
atoms 14
atom_types 2
bonds 13
bond_types 2
angles 24
angle_types 3
dihedrals 27
dihedral_types 3
dihedral_seq_size 4
impropers 0
improper_types 0
nb_size 54
nb_types 3
nb_mode 1