[gmx-users] about details of the topology file.
Mufaddal Soni
muffi_gro at yahoo.com
Mon Jan 14 17:44:04 CET 2008
Dear users,
Thankyou for helping me regarding the topology file of my FNP inhibitor. I am facing one small problem understanding the topology file of my inhibitor. I have copied a part of my topology file.
[ pairs ]
; ai aj fu c0, c1, ...
1 6 1 ; OP1 F1
1 7 1 ; OP1 F2
1 8 1 ; OP1 C8
2 9 1 ; P1 C9
2 24 1 ; P1 C7
3 6 1 ; OP2 F1
3 7 1 ; OP2 F2
3 8 1 ; OP2 C8
4 6 1 ; OP3 F1
4 7 1 ; OP3 F2
4 8 1 ; OP3 C8
5 10 1 ; C1 C10
5 23 1 ; C1 C6
6 9 1 ; F1 C9
6 24 1 ; F1 C7
7 9 1 ; F2 C9
7 24 1 ; F2 C7
8 11 1 ; C8 C11
8 22 1 ; C8 C5
9 12 1 ; C9 C2
9 21 1 ; C9 C4
9 23 1 ; C9 C6
10 13 1 ; C10 C12
10 20 1 ; C10 C3
10 24 1 ; C10 C7
11 14 1 ; C11 F3
11 15 1 ; C11 F4
11 16 1 ; C11 P2
11 21 1 ; C11 C4
11 23 1 ; C11 C6
12 17 1 ; C2 OP5
12 18 1 ; C2 OP6
12 19 1 ; C2 OP4
12 22 1 ; C2 C5
13 21 1 ; C12 C4
14 17 1 ; F3 OP5
14 18 1 ; F3 OP6
14 19 1 ; F3 OP4
14 20 1 ; F3 C3
15 17 1 ; F4 OP5
15 18 1 ; F4 OP6
15 19 1 ; F4 OP4
15 20 1 ; F4 C3
16 20 1 ; P2 C3
20 23 1 ; C3 C6
21 24 1 ; C4 C7
what i dont get here is the significance of this pairing cos there are no bonds between these atoms.
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 120.0 585.8 120.0 585.8 ; OP1 P1 OP2
1 2 4 1 120.0 585.8 120.0 585.8 ; OP1 P1 OP3
1 2 5 1 109.6 397.5 109.6 397.5 ; OP1 P1 C1
3 2 4 1 120.0 585.8 120.0 585.8 ; OP2 P1 OP3
3 2 5 1 109.6 397.5 109.6 397.5 ; OP2 P1 C1
4 2 5 1 109.6 397.5 109.6 397.5 ; OP3 P1 C1
2 5 6 1 109.5 397.5 109.5 397.5 ; P1 C1 F1
2 5 7 1 109.5 397.5 109.5 397.5 ; P1 C1 F2
2 5 8 1 109.5 397.5 109.5 397.5 ; P1 C1 C8
6 5 7 1 109.5 397.5 109.5 397.5 ; F1 C1 F2
6 5 8 1 109.5 397.5 109.5 397.5 ; F1 C1 C8
7 5 8 1 109.5 397.5 109.5 397.5 ; F2 C1 C8
5 8 9 1 120.0 418.4 120.0 418.4 ; C1 C8 C9
5 8 24 1 120.0 418.4 120.0 418.4 ; C1 C8 C7
9 8 24 1 120.0 418.4 120.0 418.4 ; C9 C8 C7
8 9 10 1 120.0 418.4 120.0 418.4 ; C8 C9 C10
9 10 11 1 120.0 418.4 120.0 418.4 ; C9 C10 C11
9 10 22 1 120.0 418.4 120.0 418.4 ; C9 C10 C5
11 10 22 1 120.0 418.4 120.0 418.4 ; C11 C10 C5
10 11 12 1 120.0 418.4 120.0 418.4 ; C10 C11 C2
11 12 13 1 120.0 418.4 120.0 418.4 ; C11 C2 C12
11 12 20 1 120.0 418.4 120.0 418.4 ; C11 C2 C3
13 12 20 1 120.0 418.4 120.0 418.4 ; C12 C2 C3
12 13 14 1 109.5 397.5 109.5 397.5 ; C2 C12 F3
12 13 15 1 109.5 397.5 109.5 397.5 ; C2 C12 F4
12 13 16 1 109.5 397.5 109.5 397.5 ; C2 C12 P2
14 13 15 1 109.5 397.5 109.5 397.5 ; F3 C12 F4
14 13 16 1 109.5 397.5 109.5 397.5 ; F3 C12 P2
15 13 16 1 109.5 397.5 109.5 397.5 ; F4 C12 P2
13 16 17 1 109.6 397.5 109.6 397.5 ; C12 P2 OP5
13 16 18 1 109.6 397.5 109.6 397.5 ; C12 P2 OP6
13 16 19 1 109.6 397.5 109.6 397.5 ; C12 P2 OP4
17 16 18 1 120.0 585.8 120.0 585.8 ; OP5 P2 OP6
17 16 19 1 120.0 585.8 120.0 585.8 ; OP5 P2 OP4
18 16 19 1 120.0 585.8 120.0 585.8 ; OP6 P2 OP4
12 20 21 1 120.0 418.4 120.0 418.4 ; C2 C3 C4
20 21 22 1 120.0 418.4 120.0 418.4 ; C3 C4 C5
10 22 21 1 120.0 418.4 120.0 418.4 ; C10 C5 C4
10 22 23 1 120.0 418.4 120.0 418.4 ; C10 C5 C6
21 22 23 1 120.0 418.4 120.0 418.4 ; C4 C5 C6
22 23 24 1 120.0 418.4 120.0 418.4 ; C5 C6 C7
8 24 23 1 120.0 418.4 120.0 418.4 ; C8 C7 C6
25 3 2 1 109.6 397.5 109.6 397.5
26 4 2 1 109.6 397.5 109.6 397.5
27 19 16 1 109.6 397.5 109.6 397.5
27 18 16 1 109.6 397.5 109.6 397.5
in this the 5th and 7th column i understand are the actual angles, but what do the 6th and 8th columns signify??
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 4 3 2 35.3 836.8 35.3 836.8 ; imp P1 OP1 OP3 OP2
5 2 6 7 2 35.3 836.8 35.3 836.8 ; imp C1 P1 F1 F2
8 5 24 9 2 0.0 1673.6 0.0 1673.6 ; imp C8 C1 C7 C9
10 22 11 9 2 0.0 1673.6 0.0 1673.6 ; imp C10 C5 C11 C9
12 20 13 11 2 0.0 1673.6 0.0 1673.6 ; imp C2 C3 C12 C11
13 12 14 15 2 35.3 836.8 35.3 836.8 ; imp C12 C2 F3 F4
16 13 17 18 2 35.3 836.8 35.3 836.8 ; imp P2 C12 OP5 OP6
22 10 23 21 2 0.0 1673.6 0.0 1673.6 ; imp C5 C10 C6 C4
8 9 10 22 2 0.0 1673.6 0.0 1673.6 ; imp C8 C9 C10 C5
9 10 22 23 2 0.0 1673.6 0.0 1673.6 ; imp C9 C10 C5 C6
10 22 23 24 2 0.0 1673.6 0.0 1673.6 ; imp C10 C5 C6 C7
22 23 24 8 2 0.0 1673.6 0.0 1673.6 ; imp C5 C6 C7 C8
23 24 8 9 2 0.0 1673.6 0.0 1673.6 ; imp C6 C7 C8 C9
24 8 9 10 2 0.0 1673.6 0.0 1673.6 ; imp C7 C8 C9 C10
10 11 12 20 2 0.0 1673.6 0.0 1673.6 ; imp C10 C11 C2 C3
11 12 20 21 2 0.0 1673.6 0.0 1673.6 ; imp C11 C2 C3 C4
12 20 21 22 2 0.0 1673.6 0.0 1673.6 ; imp C2 C3 C4 C5
20 21 22 10 2 0.0 1673.6 0.0 1673.6 ; imp C3 C4 C5 C10
21 22 10 11 2 0.0 1673.6 0.0 1673.6 ; imp C4 C5 C10 C11
22 10 11 12 2 0.0 1673.6 0.0 1673.6 ; imp C5 C10 C11 C2
1 2 5 8 1 0.0 1.0 3 0.0 1.0 3 ; dih OP1 P1 C1 C8
1 2 5 8 1 0.0 3.1 2 0.0 3.1 2 ; dih OP1 P1 C1 C8
2 5 8 24 1 0.0 1.0 3 0.0 1.0 3 ; dih P1 C1 C8 C7
2 5 8 24 1 0.0 3.1 2 0.0 3.1 2 ; dih P1 C1 C8 C7
11 12 13 16 1 0.0 1.0 3 0.0 1.0 3 ; dih C11 C2 C12 P2
11 12 13 16 1 0.0 3.1 2 0.0 3.1 2 ; dih C11 C2 C12 P2
12 13 16 19 1 0.0 1.0 3 0.0 1.0 3 ; dih C2 C12 P2 OP4
12 13 16 19 1 0.0 3.1 2 0.0 3.1 2 ; dih C2 C12 P2 OP4
Similarly here the 6th and 8th columns give the values of the dihedrals but i dont understand what the 7th and 9th column signify.
Cheers,
Mufaddal Soni.
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