[gmx-users] No default Angle types and Improper Dih. types
Lara Bunte
lara.bunte at yahoo.de
Mon Dec 26 10:22:21 CET 2011
Hello
after use of grompp I got the following errors:
ERROR 1 [file topol.top, line 172]:
No default Angle types
this error repeats
ERROR 38 [file topol.top, line 233]:
No default Improper Dih. types
this error repeats also
Excluding 3 bonded neighbours molecule type 'Isoalloxazin'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file topol.top, line 278]:
System has non-zero total charge: 0.000400
Total charge should normally be an integer.
There was 1 note
-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: /home/me/src/gromacs-4.5.5/src/kernel/grompp.c, line: 1372
Fatal error:
There were 55 errors in input file(s)
I give you my topology file. Could you please tell me what there is false?
#include "./charmm27_local.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Isoalloxazin 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 ISO rtp ISO q 0.0
1 NN3A 1
ISO N1 1 -0.6519 14.007 ; qtot -0.6519
2 CN1A 1 ISO C2 2 0.7481 12.011 ; qtot 0.0962
3 ON1 1 ISO O2 3 -0.7371 15.9994 ; qtot -0.6409
4 NN2U 1 ISO N3 4 -0.4064 14.007 ; qtot
-1.047
5 HN2 1 ISO H3 5 0.358 1.008 ; qtot -0.6893
6 CN1B 1 ISO C4 6 0.4925 12.011 ; qtot -0.1968
7 ON1 1 ISO O4 7 -0.6824 15.9994 ; qtot -0.8792
8 CN5B 1
ISO C4A 8 0.0224 12.011 ; qtot -0.8568
9 NN3A 1 ISO N5 9 -0.2742 14.007 ; qtot -1.131
10 CPTB 1 ISO C5A 10 0.1797 12.011 ; qtot -0.9513
11 CA1 1 ISO C6 11 -0.2904 12.011 ; qtot -1.242
12 HP 1 ISO H6 12 0.3012 1.008 ; qtot -0.9405
13 CA2 1 ISO C7 13 0.1958 12.011 ; qtot -0.7447
14 CA3 1 ISO C8 14 0.07 12.011 ; qtot -0.6747
15 CA4 1 ISO
C9 15 -0.0292 12.011 ; qtot -0.7039
16 HP 1 ISO H9 16 0.1949 1.008 ; qtot -0.509
17 CPTA 1 ISO C9A 17 -0.1901 12.011 ; qtot -0.6991
18 NN2G 1 ISO N10 18 0.273 14.007 ; qtot -0.4261
19
CN5A 1 ISO C0A 19 0.2618 12.011 ; qtot -0.1643
20 CT3 1 ISO C7M 20 -0.3701 12.011 ; qtot -0.5344
21 HAI 1 ISO H7A 21 0.1234 1.008 ; qtot -0.411
22 HAI 1 ISO H7B 22 0.1234
1.008 ; qtot -0.2876
23 HAI 1 ISO H7C 23 0.1234 1.008 ; qtot -0.1642
24 CT3 1 ISO C8M 24 -0.3645 12.011 ; qtot -0.5287
25 HAI 1 ISO H8A 25 0.1215 1.008 ; qtot -0.4072
26 HAI 1
ISO H8B 26 0.1215 1.008 ; qtot -0.2857
27 HAI 1 ISO H8C 27 0.1215 1.008 ; qtot -0.1642
28 CT3 1 ISO C0M 28 -0.3952 12.011 ; qtot -0.5594
29 HAI 1 ISO H0A 29 0.1318 1.008 ; qtot -0.4276
30 HAI 1 ISO H0B 30 0.1318 1.008 ; qtot -0.2958
31 HAI 1 ISO H0C 31 0.1318 1.008 ; qtot -0.164
32 HP 1 ISO H5 32 0.1644 1.008 ; qtot 0.0004
[ bonds ]
; ai aj funct
c0 c1 c2 c3
1 2 1 287.0 1.382
1 19 1 381.2 1.320
2 3 1 691.5 1.229
2 4 1 176.0 1.429
4 5 1 459.8 1.022
4 6
1 281.2 1.384
6 7 1 667.7 1.244
6 8 1 262.6 1.450
8 9 1 355.8 1.365
8 19 1 362.5 1.416
9 10 1 297.3 1.379
9 32 1 459.3 1.027
10 11 1
362.7 1.402
10 17 1 322.8 1.424
11 12 1 375.5 1.094
11 13 1 341.7 1.395
13 14 1 312.9 1.417
13 20 1 265.1 1.507
14 15 1 353.5 1.402
14 24 1 266.9 1.507
15
16 1 382.1 1.090
15 17 1 334.8 1.402
17 18 1 285.9 1.402
18 19 1 270.1 1.404
18 28 1 260.2 1.463
20 21 1 356.5 1.100
20 22 1 356.5 1.100
20 23 1 356.5
1.100
24 25 1 356.5 1.100
24 26 1 356.5 1.100
24 27 1 356.5 1.100
28 29 1 356.5 1.100
28 30 1 356.5 1.100
28 31 1 356.5 1.100
[ pairs ]
; ai aj funct c0
c1 c2 c3
1 5 1
1 6 1
1 9 1
1 17 1
1 28 1
2 7 1
2 8 1
2 18 1
3 5 1
3 6 1
3 19 1
4 9 1
4 19 1
5 7 1
5 8 1
6 10 1
6 18 1
6 32 1
7 9 1
7 19 1
8 11 1
8 17 1
8 28 1
9 12 1
9 13 1
9 15 1
9 18 1
10 14 1
10 16 1
10 19 1
10 20 1
10 28 1
11 15 1
11 18 1
11 21 1
11 22 1
11 23 1
11 24 1
11 32 1
12 14 1
12 17 1
12 20 1
13 16 1
13 17 1
13 25 1
13 26 1
13 27 1
14 18 1
14 21 1
14 22 1
14 23 1
15 19 1
15 20 1
15 25 1
15 26 1
15 27 1
15 28 1
16 18 1
16 24 1
17 24 1
17 29 1
17 30 1
17 31 1
17 32 1
19 29 1
19 30 1
19
31 1
19 32 1
20 24 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 19 1
1 2 3 1 250.00 123.75
1 2 4 1 230.00 117.47
3 2 4 1
2 4 5 1 105.00 115.95
2 4 6 1 90.00 126.44
5 4 6 1
4 6 7 1 225.00 124.66
4 6 8 1 100.00 112.38
7 6 8 1
6
8 9 1 110.00 118.06
6 8 19 1
9 8 19 1
8 9 10 1 250.00 122.10
8 9 32 1 53.75 115.50
10 9 32 1
9 10 11 1 80.00 121.96
9 10 17 1
11 10 17 1
10 11 12 1 53.75 118.46
10 11 13 1 250.00 121.72
12 11 13 1
11 13 14 1 75.00 118.68
11 13 20 1 70.00 120.23
14 13 20 1
13 14 15 1 77.00
119.56
13 14 24 1 70.50 120.72
15 14 24 1
14 15 16 1 75.00 118.45
14 15 17 1 230.00 122.24
16 15 17 1
10 17 15 1
10 17 18 1
15 17 18 1 52.25 122.22
17
18 19 1 350.00 121.14
17 18 28 1 81.25 120.07
19 18 28 1
1 19 8 1
1 19 18 1
8 19 18 1
13 20 21 1
13 20 22 1
13 20 23 1
21 20
22 1
21 20 23 1
22 20 23 1
14 24 25 1
14 24 26 1
14 24 27 1
25 24 26 1
25 24 27 1
26 24 27 1
18 28 29 1
18 28 30 1
18 28
31 1
29 28 30 1
29 28 31 1
30 28 31 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
19 1 2 3 2
2 1 19 8 2
1 2 4 6 2
2 4 6 7 2
4 6 8 9 2
6 8 9 10 2
6 8 19 1 2
8 9 10 11 2
9 10 11 13
2
9 10 17 15 2
10 11 13 14 2
11 13 14 15 2
11 13 20 21 2
13 14 15 17 2
13 14 24 25 2
14 15 17 10 2
10 17 18 19 2
17 18 19
1 2
17 18 28 29 2
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "./charmm27_local.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "./charmm27_local.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound
#mols
Isoalloxazin 1
SOL 606
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