[gmx-users] topology files generated with PRODRG and ffG43a1bon.itp coding
Aina Quintilla
aina.quintilla at int.fzk.de
Tue Feb 15 18:34:16 CET 2005
dear gromacs´ users,
i have generated a topology file for a dye (that i want to attach to a
protein) with PRODRG but i do not know what is the relation between the
values given for the bonds angles and dihedrals and the gb_XX ga_XX and
gd_XX..
the dye and the protein should belong to the same molecule.. so i should
"unificate" the top file??
thank you;
i include the part of the top file that defines bonds angles and dihedrals
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.143 251040.0 0.143 251040.0 ; CAT OBQ
2 3 1 0.136 376560.0 0.136 376560.0 ; OBQ CBP
3 4 1 0.139 418400.0 0.139 418400.0 ; CBP CBR
3 6 1 0.139 418400.0 0.139 418400.0 ; CBP CBO
4 5 1 0.139 418400.0 0.139 418400.0 ; CBR CBL
5 8 1 0.139 418400.0 0.139 418400.0 ; CBL CBM
6 7 1 0.139 418400.0 0.139 418400.0 ; CBO CBN
7 8 1 0.139 418400.0 0.139 418400.0 ; CBN CBM
8 9 1 0.139 418400.0 0.139 418400.0 ; CBM CBG
9 10 1 0.133 418400.0 0.133 418400.0 ; CBG CBF
9 14 1 0.140 334720.0 0.140 334720.0 ; CBG NAW
10 11 1 0.133 418400.0 0.133 418400.0 ; CBF CAV
11 12 1 0.133 418400.0 0.133 418400.0 ; CAV CAU
12 13 1 0.139 418400.0 0.139 418400.0 ; CAU CAX
12 14 1 0.140 334720.0 0.140 334720.0 ; CAU NAW
13 20 1 0.139 418400.0 0.139 418400.0 ; CAX CAY
14 15 1 0.148 334720.0 0.148 334720.0 ; NAW CBC
15 16 1 0.133 338262.1 0.133 338262.1 ; CBC FBD
15 17 1 0.133 338262.1 0.133 338262.1 ; CBC FBE
15 18 1 0.148 334720.0 0.148 334720.0 ; CBC NBB
18 19 1 0.133 418400.0 0.133 418400.0 ; NBB CBH
18 20 1 0.140 334720.0 0.140 334720.0 ; NBB CAY
19 23 1 0.133 418400.0 0.133 418400.0 ; CBH CBI
20 21 1 0.139 418400.0 0.139 418400.0 ; CAY CAZ
21 22 1 0.153 334720.0 0.153 334720.0 ; CAZ CBA
21 23 1 0.139 418400.0 0.139 418400.0 ; CAZ CBI
23 24 1 0.153 334720.0 0.153 334720.0 ; CBI CBJ
24 25 1 0.153 334720.0 0.153 334720.0 ; CBJ CBK
25 26 1 0.153 334720.0 0.153 334720.0 ; CBK CAQ
26 27 1 0.123 502080.0 0.123 502080.0 ; CAQ OAS
26 28 1 0.133 418400.0 0.133 418400.0 ; CAQ NAR
28 29 1 0.100 374468.0 0.100 374468.0 ; NAR HAE
28 30 1 0.147 376560.0 0.147 376560.0 ; NAR CAP
30 31 1 0.153 334720.0 0.153 334720.0 ; CAP CAL
31 32 1 0.153 334720.0 0.153 334720.0 ; CAL CAM
32 33 1 0.153 334720.0 0.153 334720.0 ; CAM CAN
33 34 1 0.153 334720.0 0.153 334720.0 ; CAN CAO
34 35 1 0.153 334720.0 0.153 334720.0 ; CAO CAI
35 36 1 0.123 502080.0 0.123 502080.0 ; CAI OAK
35 37 1 0.133 418400.0 0.133 418400.0 ; CAI NAJ
37 38 1 0.100 374468.0 0.100 374468.0 ; NAJ HAD
37 39 1 0.147 376560.0 0.147 376560.0 ; NAJ CAH
39 40 1 0.153 334720.0 0.153 334720.0 ; CAH CAG
40 41 1 0.153 334720.0 0.153 334720.0 ; CAG CAF
41 42 1 0.153 334720.0 0.153 334720.0 ; CAF CB
42 43 1 0.153 334720.0 0.153 334720.0 ; CB CA
43 44 1 0.153 334720.0 0.153 334720.0 ; CA C
43 46 1 0.147 376560.0 0.147 376560.0 ; CA N
44 45 1 0.123 502080.0 0.123 502080.0 ; C O
46 47 1 0.100 374468.0 0.100 374468.0 ; N HAB
46 48 1 0.100 374468.0 0.100 374468.0 ; N HAC
46 49 1 0.100 374468.0 0.100 374468.0 ; N HAA
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; CAT CBR
1 6 1 ; CAT CBO
2 5 1 ; OBQ CBL
2 7 1 ; OBQ CBN
3 8 1 ; CBP CBM
4 7 1 ; CBR CBN
4 9 1 ; CBR CBG
5 6 1 ; CBL CBO
5 10 1 ; CBL CBF
5 14 1 ; CBL NAW
6 9 1 ; CBO CBG
7 10 1 ; CBN CBF
7 14 1 ; CBN NAW
8 11 1 ; CBM CAV
8 12 1 ; CBM CAU
8 15 1 ; CBM CBC
9 13 1 ; CBG CAX
9 16 1 ; CBG FBD
9 17 1 ; CBG FBE
9 18 1 ; CBG NBB
10 13 1 ; CBF CAX
10 15 1 ; CBF CBC
11 15 1 ; CAV CBC
11 20 1 ; CAV CAY
12 16 1 ; CAU FBD
12 17 1 ; CAU FBE
12 18 1 ; CAU NBB
12 21 1 ; CAU CAZ
13 15 1 ; CAX CBC
13 19 1 ; CAX CBH
13 22 1 ; CAX CBA
13 23 1 ; CAX CBI
14 19 1 ; NAW CBH
14 20 1 ; NAW CAY
15 21 1 ; CBC CAZ
15 23 1 ; CBC CBI
16 19 1 ; FBD CBH
16 20 1 ; FBD CAY
17 19 1 ; FBE CBH
17 20 1 ; FBE CAY
18 22 1 ; NBB CBA
18 24 1 ; NBB CBJ
19 22 1 ; CBH CBA
19 25 1 ; CBH CBK
20 24 1 ; CAY CBJ
21 25 1 ; CAZ CBK
22 24 1 ; CBA CBJ
23 26 1 ; CBI CAQ
24 27 1 ; CBJ OAS
24 28 1 ; CBJ NAR
25 29 1 ; CBK HAE
25 30 1 ; CBK CAP
26 31 1 ; CAQ CAL
27 29 1 ; OAS HAE
27 30 1 ; OAS CAP
28 32 1 ; NAR CAM
29 31 1 ; HAE CAL
30 33 1 ; CAP CAN
31 34 1 ; CAL CAO
32 35 1 ; CAM CAI
33 36 1 ; CAN OAK
33 37 1 ; CAN NAJ
34 38 1 ; CAO HAD
34 39 1 ; CAO CAH
35 40 1 ; CAI CAG
36 38 1 ; OAK HAD
36 39 1 ; OAK CAH
37 41 1 ; NAJ CAF
38 40 1 ; HAD CAG
39 42 1 ; CAH CB
40 43 1 ; CAG CA
41 44 1 ; CAF C
41 46 1 ; CAF N
42 45 1 ; CB O
42 47 1 ; CB HAB
42 48 1 ; CB HAC
42 49 1 ; CB HAA
44 47 1 ; C HAB
44 48 1 ; C HAC
44 49 1 ; C HAA
45 46 1 ; O N
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 109.5 334.7 109.5 334.7 ; CAT OBQ CBP
2 3 4 1 120.0 418.4 120.0 418.4 ; OBQ CBP CBR
2 3 6 1 120.0 418.4 120.0 418.4 ; OBQ CBP CBO
4 3 6 1 120.0 418.4 120.0 418.4 ; CBR CBP CBO
3 4 5 1 120.0 418.4 120.0 418.4 ; CBP CBR CBL
4 5 8 1 120.0 418.4 120.0 418.4 ; CBR CBL CBM
3 6 7 1 120.0 418.4 120.0 418.4 ; CBP CBO CBN
6 7 8 1 120.0 418.4 120.0 418.4 ; CBO CBN CBM
5 8 7 1 120.0 418.4 120.0 418.4 ; CBL CBM CBN
5 8 9 1 120.0 418.4 120.0 418.4 ; CBL CBM CBG
7 8 9 1 120.0 418.4 120.0 418.4 ; CBN CBM CBG
8 9 10 1 126.0 418.4 126.0 418.4 ; CBM CBG CBF
8 9 14 1 120.0 418.4 120.0 418.4 ; CBM CBG NAW
10 9 14 1 108.0 418.4 108.0 418.4 ; CBF CBG NAW
9 10 11 1 108.0 418.4 108.0 418.4 ; CBG CBF CAV
10 11 12 1 108.0 418.4 108.0 418.4 ; CBF CAV CAU
11 12 13 1 132.0 418.4 132.0 418.4 ; CAV CAU CAX
11 12 14 1 108.0 418.4 108.0 418.4 ; CAV CAU NAW
13 12 14 1 120.0 418.4 120.0 418.4 ; CAX CAU NAW
12 13 20 1 120.0 418.4 120.0 418.4 ; CAU CAX CAY
9 14 12 1 108.0 418.4 108.0 418.4 ; CBG NAW CAU
9 14 15 1 132.0 418.4 132.0 418.4 ; CBG NAW CBC
12 14 15 1 120.0 418.4 120.0 418.4 ; CAU NAW CBC
14 15 16 1 109.5 397.5 109.5 397.5 ; NAW CBC FBD
14 15 17 1 109.5 397.5 109.5 397.5 ; NAW CBC FBE
14 15 18 1 109.5 397.5 109.5 397.5 ; NAW CBC NBB
16 15 17 1 109.5 397.5 109.5 397.5 ; FBD CBC FBE
16 15 18 1 109.5 397.5 109.5 397.5 ; FBD CBC NBB
17 15 18 1 109.5 397.5 109.5 397.5 ; FBE CBC NBB
15 18 19 1 132.0 418.4 132.0 418.4 ; CBC NBB CBH
15 18 20 1 120.0 418.4 120.0 418.4 ; CBC NBB CAY
19 18 20 1 108.0 418.4 108.0 418.4 ; CBH NBB CAY
18 19 23 1 108.0 418.4 108.0 418.4 ; NBB CBH CBI
13 20 18 1 120.0 418.4 120.0 418.4 ; CAX CAY NBB
13 20 21 1 132.0 418.4 132.0 418.4 ; CAX CAY CAZ
18 20 21 1 108.0 418.4 108.0 418.4 ; NBB CAY CAZ
20 21 22 1 120.0 418.4 120.0 418.4 ; CAY CAZ CBA
20 21 23 1 108.0 418.4 108.0 418.4 ; CAY CAZ CBI
22 21 23 1 120.0 418.4 120.0 418.4 ; CBA CAZ CBI
19 23 21 1 108.0 418.4 108.0 418.4 ; CBH CBI CAZ
19 23 24 1 126.0 418.4 126.0 418.4 ; CBH CBI CBJ
21 23 24 1 126.0 418.4 126.0 418.4 ; CAZ CBI CBJ
23 24 25 1 111.0 460.2 111.0 460.2 ; CBI CBJ CBK
24 25 26 1 111.0 460.2 111.0 460.2 ; CBJ CBK CAQ
25 26 27 1 121.0 502.1 121.0 502.1 ; CBK CAQ OAS
25 26 28 1 115.0 502.1 115.0 502.1 ; CBK CAQ NAR
27 26 28 1 124.0 502.1 124.0 502.1 ; OAS CAQ NAR
26 28 29 1 123.0 292.9 123.0 292.9 ; CAQ NAR HAE
26 28 30 1 122.0 502.1 122.0 502.1 ; CAQ NAR CAP
29 28 30 1 115.0 376.6 115.0 376.6 ; HAE NAR CAP
28 30 31 1 109.5 460.2 109.5 460.2 ; NAR CAP CAL
30 31 32 1 111.0 460.2 111.0 460.2 ; CAP CAL CAM
31 32 33 1 111.0 460.2 111.0 460.2 ; CAL CAM CAN
32 33 34 1 111.0 460.2 111.0 460.2 ; CAM CAN CAO
33 34 35 1 111.0 460.2 111.0 460.2 ; CAN CAO CAI
34 35 36 1 121.0 502.1 121.0 502.1 ; CAO CAI OAK
34 35 37 1 115.0 502.1 115.0 502.1 ; CAO CAI NAJ
36 35 37 1 124.0 502.1 124.0 502.1 ; OAK CAI NAJ
35 37 38 1 123.0 292.9 123.0 292.9 ; CAI NAJ HAD
35 37 39 1 122.0 502.1 122.0 502.1 ; CAI NAJ CAH
38 37 39 1 115.0 376.6 115.0 376.6 ; HAD NAJ CAH
37 39 40 1 109.5 460.2 109.5 460.2 ; NAJ CAH CAG
39 40 41 1 111.0 460.2 111.0 460.2 ; CAH CAG CAF
40 41 42 1 111.0 460.2 111.0 460.2 ; CAG CAF CB
41 42 43 1 111.0 460.2 111.0 460.2 ; CAF CB CA
42 43 44 1 109.5 460.2 109.5 460.2 ; CB CA C
42 43 46 1 109.5 460.2 109.5 460.2 ; CB CA N
44 43 46 1 109.5 460.2 109.5 460.2 ; C CA N
43 44 45 1 121.0 502.1 121.0 502.1 ; CA C O
43 46 47 1 109.5 376.6 109.5 376.6 ; CA N HAB
43 46 48 1 109.5 376.6 109.5 376.6 ; CA N HAC
43 46 49 1 109.5 376.6 109.5 376.6 ; CA N HAA
47 46 48 1 109.5 334.7 109.5 334.7 ; HAB N HAC
47 46 49 1 109.5 334.7 109.5 334.7 ; HAB N HAA
48 46 49 1 109.5 334.7 109.5 334.7 ; HAC N HAA
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
3 2 6 4 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBP OBQ CBO
CBR
8 9 7 5 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBM CBG CBN
CBL
9 8 14 10 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBG CBM NAW
CBF
12 14 13 11 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CAU NAW CAX
CAV
14 15 12 9 2 0.0 1673.6 0 0.0 1673.6 0 ; imp NAW CBC CAU
CBG
18 15 19 20 2 0.0 1673.6 0 0.0 1673.6 0 ; imp NBB CBC CBH
CAY
20 21 18 13 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CAY CAZ NBB
CAX
21 20 23 22 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CAZ CAY CBI
CBA
23 19 21 24 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBI CBH CAZ
CBJ
26 25 28 27 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CAQ CBK NAR
OAS
28 26 29 30 2 0.0 1673.6 0 0.0 1673.6 0 ; imp NAR CAQ HAE
CAP
35 34 37 36 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CAI CAO NAJ
OAK
37 35 38 39 2 0.0 1673.6 0 0.0 1673.6 0 ; imp NAJ CAI HAD
CAH
15 14 17 16 2 35.3 836.8 0 35.3 836.8 0 ; imp CBC NAW FBE
FBD
43 42 44 46 2 35.3 836.8 0 35.3 836.8 0 ; imp CA CB C
N
46 43 48 47 2 35.3 836.8 0 35.3 836.8 0 ; imp N CA HAC
HAB
18 19 23 21 2 0.0 1673.6 0 0.0 1673.6 0 ; imp NBB CBH CBI
CAZ
19 23 21 20 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBH CBI CAZ
CAY
23 21 20 18 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBI CAZ CAY
NBB
21 20 18 19 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CAZ CAY NBB
CBH
20 18 19 23 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CAY NBB CBH
CBI
9 10 11 12 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBG CBF CAV
CAU
10 11 12 14 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBF CAV CAU
NAW
11 12 14 9 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CAV CAU NAW
CBG
12 14 9 10 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CAU NAW CBG
CBF
14 9 10 11 2 0.0 1673.6 0 0.0 1673.6 0 ; imp NAW CBG CBF
CAV
3 4 5 8 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBP CBR CBL
CBM
4 5 8 7 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBR CBL CBM
CBN
5 8 7 6 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBL CBM CBN
CBO
8 7 6 3 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBM CBN CBO
CBP
7 6 3 4 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBN CBO CBP
CBR
6 3 4 5 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CBO CBP CBR
CBL
6 3 2 1 1 0.0 3.8 6 0.0 3.8 6 ; dih CBO CBP OBQ
CAT
5 8 9 14 1 180.0 5.9 2 180.0 5.9 2 ; dih CBL CBM CBG
NAW
11 12 13 20 1 180.0 41.8 2 180.0 41.8 2 ; dih CAV CAU CAX
CAY
21 20 13 12 1 180.0 41.8 2 180.0 41.8 2 ; dih CAZ CAY CAX
CAU
9 14 15 18 1 0.0 0.4 6 0.0 0.4 6 ; dih CBG NAW CBC
NBB
14 15 18 20 1 0.0 0.4 6 0.0 0.4 6 ; dih NAW CBC NBB
CAY
19 23 24 25 1 0.0 0.4 6 0.0 0.4 6 ; dih CBH CBI CBJ
CBK
26 25 24 23 1 0.0 5.9 3 0.0 5.9 3 ; dih CAQ CBK CBJ
CBI
24 25 26 28 1 0.0 0.4 6 0.0 0.4 6 ; dih CBJ CBK CAQ
NAR
25 26 28 30 1 180.0 33.5 2 180.0 33.5 2 ; dih CBK CAQ NAR
CAP
31 30 28 26 1 180.0 0.4 6 180.0 0.4 6 ; dih CAL CAP NAR
CAQ
32 31 30 28 1 0.0 5.9 3 0.0 5.9 3 ; dih CAM CAL CAP
NAR
33 32 31 30 1 0.0 5.9 3 0.0 5.9 3 ; dih CAN CAM CAL
CAP
34 33 32 31 1 0.0 5.9 3 0.0 5.9 3 ; dih CAO CAN CAM
CAL
35 34 33 32 1 0.0 5.9 3 0.0 5.9 3 ; dih CAI CAO CAN
CAM
33 34 35 37 1 0.0 0.4 6 0.0 0.4 6 ; dih CAN CAO CAI
NAJ
34 35 37 39 1 180.0 33.5 2 180.0 33.5 2 ; dih CAO CAI NAJ
CAH
40 39 37 35 1 180.0 0.4 6 180.0 0.4 6 ; dih CAG CAH NAJ
CAI
41 40 39 37 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF CAG CAH
NAJ
42 41 40 39 1 0.0 5.9 3 0.0 5.9 3 ; dih CB CAF CAG
CAH
43 42 41 40 1 0.0 5.9 3 0.0 5.9 3 ; dih CA CB CAF
CAG
41 42 43 46 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF CB CA
N
42 43 44 45 1 0.0 0.4 6 0.0 0.4 6 ; dih CB CA C
O
42 43 46 49 1 0.0 3.8 3 0.0 3.8 3 ; dih CB CA N
HAA
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
[ molecules ]
; Compound #mols
Protein 1
SOL 429
More information about the gromacs.org_gmx-users
mailing list