[gmx-users] No default Angle types and Improper Dih. types
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Dec 26 13:38:32 CET 2011
On 12/26/2011 8:22 PM, Lara Bunte wrote:
> Hello
> after use of grompp I got the following errors:
>
> ERROR 1 [file topol.top, line 172]:
> No default Angle types
grompp needs either parameters for the angle interaction on the line it
is defined, or one able to be looked up from the [angletypes] section
using the atom types of the atoms that define the interaction. Neither
of these were available, so grompp flags the error. You will need to do
some detective work based on the contents of line 172 (and the other
such lines) to work out why this is so.
Mark
>
> 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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