[gmx-users] about details of the topology file.
Jochen Hub
jhub at gwdg.de
Mon Jan 14 19:48:03 CET 2008
Check the manual, Chapter 5. All expained there.
Cheers, Jochen
Mufaddal Soni wrote:
> 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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--
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
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