Dear users,<br> 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.<br><br>[ pairs ]<br>; ai aj fu c0, c1, ...<br> 1 6 1 ; OP1 F1 <br> 1 7
1 ; OP1 F2 <br> 1 8 1 ; OP1 C8 <br> 2 9 1 ; P1
C9 <br> 2 24 1 ; P1 C7 <br> 3 6 1 ; OP2 F1 <br> 3 7
1 ; OP2 F2 <br> 3 8 1 ; OP2 C8 <br> 4 6 1 ; OP3 F1
<br> 4 7 1 ; OP3 F2 <br> 4 8 1 ; OP3 C8 <br> 5 10 1
; C1 C10 <br> 5 23 1 ; C1 C6 <br> 6 9 1 ; F1 C9 <br> 6 24
1 ; F1 C7 <br> 7 9 1 ; F2 C9 <br> 7 24 1 ; F2
C7 <br> 8 11 1 ; C8 C11 <br> 8 22 1 ; C8 C5 <br> 9 12
1 ; C9 C2 <br> 9 21 1 ; C9 C4 <br> 9 23 1 ; C9
C6 <br> 10 13 1 ; C10 C12 <br> 10 20 1 ; C10 C3 <br> 10 24 1 ;
C10 C7 <br> 11 14 1 ; C11 F3 <br> 11 15 1 ; C11 F4 <br> 11 16 1
; C11 P2 <br> 11 21 1 ; C11 C4 <br> 11 23 1 ; C11 C6 <br> 12 17
1 ; C2 OP5 <br> 12 18 1 ; C2 OP6 <br> 12 19 1 ; C2 OP4 <br> 12
22 1 ; C2 C5 <br> 13 21 1 ; C12 C4 <br> 14 17 1 ; F3 OP5
<br> 14 18 1 ; F3 OP6 <br> 14 19 1 ; F3 OP4 <br> 14 20 1 ;
F3 C3 <br> 15 17 1 ; F4 OP5 <br> 15 18 1 ; F4 OP6 <br> 15 19 1
; F4 OP4 <br> 15 20 1 ; F4 C3 <br> 16 20 1 ; P2 C3 <br> 20 23
1 ; C3 C6 <br> 21 24 1 ; C4 C7 <br>what i dont get here is the significance of this pairing cos there are no bonds between these atoms.<br><br>[ angles ]<br>; ai aj ak fu c0, c1, ...<br> 1 2 3 1 120.0 585.8
120.0 585.8 ; OP1 P1 OP2 <br> 1 2 4 1 120.0 585.8 120.0 585.8 ; OP1 P1 OP3 <br> 1 2 5 1 109.6 397.5 109.6 397.5 ; OP1 P1 C1 <br> 3 2 4 1 120.0 585.8 120.0 585.8 ; OP2 P1 OP3 <br> 3 2 5 1 109.6
397.5 109.6 397.5 ; OP2 P1 C1 <br> 4 2 5 1 109.6 397.5 109.6 397.5 ; OP3 P1 C1 <br> 2 5 6 1 109.5 397.5 109.5 397.5 ; P1 C1 F1 <br> 2 5 7 1 109.5 397.5 109.5 397.5 ; P1 C1 F2 <br> 2 5 8 1
109.5 397.5 109.5 397.5 ; P1 C1 C8 <br> 6 5 7 1 109.5 397.5 109.5 397.5 ; F1 C1 F2 <br> 6 5 8 1 109.5 397.5 109.5 397.5 ; F1 C1 C8 <br> 7 5 8 1 109.5 397.5 109.5 397.5 ; F2 C1 C8 <br> 5
8 9 1 120.0 418.4 120.0 418.4 ; C1 C8 C9 <br> 5 8 24 1 120.0 418.4 120.0 418.4 ; C1 C8 C7 <br> 9 8 24 1 120.0 418.4 120.0 418.4 ; C9 C8 C7 <br> 8 9 10 1 120.0 418.4 120.0 418.4 ; C8 C9 C10
<br> 9 10 11 1 120.0 418.4 120.0 418.4 ; C9 C10 C11 <br> 9 10 22 1 120.0 418.4 120.0 418.4 ; C9 C10 C5 <br> 11 10 22 1 120.0 418.4 120.0 418.4 ; C11 C10 C5 <br> 10 11 12 1 120.0 418.4 120.0 418.4 ; C10 C11 C2 <br> 11 12
13 1 120.0 418.4 120.0 418.4 ; C11 C2 C12 <br> 11 12 20 1 120.0 418.4 120.0 418.4 ; C11 C2 C3 <br> 13 12 20 1 120.0 418.4 120.0 418.4 ; C12 C2 C3 <br> 12 13 14 1 109.5 397.5 109.5 397.5 ; C2 C12 F3 <br> 12 13 15 1
109.5 397.5 109.5 397.5 ; C2 C12 F4 <br> 12 13 16 1 109.5 397.5 109.5 397.5 ; C2 C12 P2 <br> 14 13 15 1 109.5 397.5 109.5 397.5 ; F3 C12 F4 <br> 14 13 16 1 109.5 397.5 109.5 397.5 ; F3 C12 P2 <br> 15 13 16 1
109.5 397.5 109.5 397.5 ; F4 C12 P2 <br> 13 16 17 1 109.6 397.5 109.6 397.5 ; C12 P2 OP5 <br> 13 16 18 1 109.6 397.5 109.6 397.5 ; C12 P2 OP6 <br> 13 16 19 1 109.6 397.5 109.6 397.5 ; C12 P2 OP4 <br> 17 16 18 1 120.0
585.8 120.0 585.8 ; OP5 P2 OP6 <br> 17 16 19 1 120.0 585.8 120.0 585.8 ; OP5 P2 OP4 <br> 18 16 19 1 120.0 585.8 120.0 585.8 ; OP6 P2 OP4 <br> 12 20 21 1 120.0 418.4 120.0 418.4 ; C2 C3 C4 <br> 20 21 22 1 120.0 418.4
120.0 418.4 ; C3 C4 C5 <br> 10 22 21 1 120.0 418.4 120.0 418.4 ; C10 C5 C4 <br> 10 22 23 1 120.0 418.4 120.0 418.4 ; C10 C5 C6 <br> 21 22 23 1 120.0 418.4 120.0 418.4 ; C4 C5 C6 <br> 22 23 24 1 120.0 418.4
120.0 418.4 ; C5 C6 C7 <br> 8 24 23 1 120.0 418.4 120.0 418.4 ; C8 C7 C6 <br> 25 3 2 1 109.6 397.5 109.6 397.5 <br> 26 4 2 1 109.6 397.5 109.6 397.5<br> 27 19 16 1 109.6 397.5 109.6 397.5<br> 27 18 16 1
109.6 397.5 109.6 397.5<br>in this the 5th and 7th column i understand are the actual angles, but what do the 6th and 8th columns signify??<br><br>[ dihedrals ]<br>; ai aj ak al fu c0, c1, m, ...<br> 2 1 4 3 2 35.3 836.8 35.3 836.8 ; imp P1 OP1 OP3 OP2 <br> 5 2 6 7 2 35.3 836.8 35.3 836.8 ; imp C1 P1 F1 F2 <br> 8 5 24 9 2 0.0
1673.6 0.0 1673.6 ; imp C8 C1 C7 C9 <br> 10 22 11 9 2 0.0 1673.6 0.0 1673.6 ; imp C10 C5 C11 C9 <br> 12 20 13 11 2 0.0 1673.6 0.0 1673.6 ; imp C2 C3 C12 C11 <br> 13 12 14 15 2 35.3 836.8 35.3 836.8 ; imp C12 C2 F3 F4 <br> 16 13 17 18 2 35.3
836.8 35.3 836.8 ; imp P2 C12 OP5 OP6 <br> 22 10 23 21 2 0.0 1673.6 0.0 1673.6 ; imp C5 C10 C6 C4 <br> 8 9 10 22 2 0.0 1673.6 0.0 1673.6 ; imp C8 C9 C10 C5 <br> 9 10 22 23 2 0.0 1673.6 0.0 1673.6 ; imp C9 C10 C5 C6 <br> 10 22 23 24 2 0.0
1673.6 0.0 1673.6 ; imp C10 C5 C6 C7 <br> 22 23 24 8 2 0.0 1673.6 0.0 1673.6 ; imp C5 C6 C7 C8 <br> 23 24 8 9 2 0.0 1673.6 0.0 1673.6 ; imp C6 C7 C8 C9 <br> 24 8 9 10 2 0.0 1673.6 0.0 1673.6 ; imp C7 C8 C9 C10 <br> 10 11 12 20
2 0.0 1673.6 0.0 1673.6 ; imp C10 C11 C2 C3 <br> 11 12 20 21 2 0.0 1673.6 0.0 1673.6 ; imp C11 C2 C3 C4 <br> 12 20 21 22 2 0.0 1673.6 0.0 1673.6 ; imp C2 C3 C4 C5 <br> 20 21 22 10 2 0.0 1673.6 0.0 1673.6 ; imp C3 C4 C5 C10 <br> 21 22 10 11
2 0.0 1673.6 0.0 1673.6 ; imp C4 C5 C10 C11 <br> 22 10 11 12 2 0.0 1673.6 0.0 1673.6 ; imp C5 C10 C11 C2 <br> 1 2 5 8 1 0.0 1.0 3 0.0 1.0 3 ; dih OP1 P1 C1 C8 <br> 1 2 5 8 1 0.0 3.1 2 0.0 3.1 2 ; dih OP1 P1 C1 C8 <br> 2
5 8 24 1 0.0 1.0 3 0.0 1.0 3 ; dih P1 C1 C8 C7 <br> 2 5 8 24 1 0.0 3.1 2 0.0 3.1 2 ; dih P1 C1 C8 C7 <br> 11 12 13 16 1 0.0 1.0 3 0.0 1.0 3 ; dih C11 C2 C12 P2 <br> 11 12 13 16 1 0.0 3.1 2 0.0 3.1 2 ; dih C11 C2 C12
P2 <br> 12 13 16 19 1 0.0 1.0 3 0.0 1.0 3 ; dih C2 C12 P2 OP4 <br> 12 13 16 19 1 0.0 3.1 2 0.0 3.1 2 ; dih C2 C12 P2 OP4 <br><br><br>Similarly here the 6th and 8th columns give the values of the dihedrals but i dont understand what the 7th and 9th column signify.<br><br>Cheers,<br>Mufaddal Soni.<br><p> 
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