No defaultt bond/dihedral etc. type for nonstandard residue GLYM

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1

GROMACS version: 2019
GROMACS modification: No
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My protein has a GLYM residue for which I am using CHARMM36 2019 forcefield. The bondtypes defined in .rtp file has included bond between N and C1, instead of that I am getting errors like there is no default bond types by grompp.

.rtp file liiks like

[ GLYM ]
[ atoms ]
N NH1 -0.470 0
HN H 0.310 1
CA CT2 -0.020 2
HA1 HB2 0.090 3
HA2 HB2 0.090 4
C C 0.510 5
O O -0.510 6
C1 C 0.550 7
O1 O -0.600 8
C2 CTL2 -0.070 9
H2A HAL2 0.060 10
H2B HAL2 0.060 11
C3 CTL2 -0.180 12
H3A HAL2 0.090 13
H3B HAL2 0.090 14
C4 CTL2 -0.180 15
H4A HAL2 0.090 16
H4B HAL2 0.090 17
C5 CTL2 -0.180 18
H5A HAL2 0.090 19
H5B HAL2 0.090 20
C6 CTL2 -0.180 21
H6A HAL2 0.090 22
H6B HAL2 0.090 23
C7 CTL2 -0.180 24
H7A HAL2 0.090 25
H7B HAL2 0.090 26
C8 CTL2 -0.180 27
H8A HAL2 0.090 28
H8B HAL2 0.090 29
C9 CTL2 -0.180 30
H9A HAL2 0.090 31
H9B HAL2 0.090 32
C10 CTL2 -0.180 33
H10A HAL2 0.090 34
H10B HAL2 0.090 35
C11 CTL2 -0.180 36
H11A HAL2 0.090 37
H11B HAL2 0.090 38
C12 CTL2 -0.180 39
H12A HAL2 0.090 40
H12B HAL2 0.090 41
C13 CTL2 -0.180 42
H13A HAL2 0.090 43
H13B HAL2 0.090 44
C14 CTL3 -0.270 45
H14A HAL3 0.090 46
H14B HAL3 0.090 47
H14C HAL3 0.090 48
[ bonds ]
N HN
N CA
C CA
C +N
CA HA1
CA HA2
N C1
C1 C2
C2 H2A
C2 H2B
C2 C3
C3 H3A
C3 H3B
C3 C4
C4 H4A
C4 H4B
C4 C5
C5 H5A
C5 H5B
C5 C6
C6 H6A
C6 H6B
C6 C7
C7 H7A
C7 H7B
C7 C8
C8 H8A
C8 H8B
C8 C9
C9 H9A
C9 H9B
C9 C10
C10 H10A
C10 H10B
C10 C11
C11 H11A
C11 H11B
C11 C12
C12 H12A
C12 H12B
C12 C13
C13 H13A
C13 H13B
C13 C14
C14 H14A
C14 H14B
C14 H14C
O C
C1 O1
[ impropers ]
C1 O1 N C2
N C1 CA HN
C CA +N O

My gro file looks like

2GLYM     N    1   8.098  15.083  26.259
2GLYM    H1    2   8.040  15.060  26.180
2GLYM    H2    3   8.041  15.093  26.340
2GLYM    H3    4   8.146  15.169  26.240
2GLYM    CA    5   8.194  14.978  26.280
2GLYM   HA1    6   8.249  14.964  26.189
2GLYM   HA2    7   8.149  14.885  26.311
2GLYM     C    8   8.281  15.017  26.400
2GLYM     O    9   8.253  14.995  26.522
2GLYM    C1   10   8.006  15.090  26.169
2GLYM    O1   11   7.920  15.177  26.179
2GLYM    C2   12   7.986  14.984  26.064
2GLYM   H2A   13   7.943  14.890  26.107
2GLYM   H2B   14   8.085  14.973  26.017
2GLYM    C3   15   7.892  15.025  25.950
2GLYM   H3A   16   7.938  15.106  25.890
2GLYM   H3B   17   7.793  15.052  25.995
2GLYM    C4   18   7.866  14.909  25.849
2GLYM   H4A   19   7.831  14.825  25.913
2GLYM   H4B   20   7.968  14.887  25.815
2GLYM    C5   21   7.765  14.937  25.741
2GLYM   H5A   22   7.778  15.036  25.693
2GLYM   H5B   23   7.665  14.954  25.788
2GLYM    C6   24   7.767  14.811  25.649
2GLYM   H6A   25   7.765  14.722  25.715
2GLYM   H6B   26   7.860  14.813  25.587
2GLYM    C7   27   7.643  14.798  25.551
2GLYM   H7A   28   7.542  14.794  25.599
2GLYM   H7B   29   7.657  14.701  25.500
2GLYM    C8   30   7.648  14.895  25.436
2GLYM   H8A   31   7.711  14.851  25.355
2GLYM   H8B   32   7.701  14.988  25.468
2GLYM    C9   33   7.511  14.929  25.378
2GLYM   H9A   34   7.539  14.974  25.279
2GLYM   H9B   35   7.464  15.012  25.434
2GLYM   C10   36   7.420  14.806  25.358
2GLYM  H10A   37   7.392  14.761  25.456
2GLYM  H10B   38   7.464  14.715  25.312
2GLYM   C11   39   7.283  14.846  25.298
2GLYM  H11A   40   7.237  14.762  25.241
2GLYM  H11B   41   7.312  14.918  25.217
2GLYM   C12   42   7.181  14.895  25.397
2GLYM  H12A   43   7.236  14.972  25.453
2GLYM  H12B   44   7.161  14.823  25.479
2GLYM   C13   45   7.060  14.962  25.346
2GLYM  H13A   46   7.090  15.053  25.289
2GLYM  H13B   47   6.996  15.012  25.423
2GLYM   C14   48   6.968  14.874  25.258
2GLYM  H14A   49   6.892  14.945  25.220
2GLYM  H14B   50   7.026  14.837  25.170
2GLYM  H14C   51   6.920  14.791  25.314

Could you please help me with this

2

Change your .rtp text here to preformatted text so it is much easier to read.

What is the exact error message you are getting? Copy and paste it.

3

The error msg is:

Fatal error:
Residue 1 named GLYM of a molecule in the input file was mapped
to an entry in the topology database, but the atom HN used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

The .gro file I provided was generated by -missing, it included NH3 but that was wrong

The original pdb file looks like

ATOM 1 N GLYMX 2 78.163 157.289 218.846 0.00 0.00
ATOM 2 HN GLYMX 2 78.183 158.100 219.421 0.00 0.00
ATOM 3 CA GLYMX 2 79.121 156.241 219.062 0.00 0.00
ATOM 4 HA1 GLYMX 2 79.673 156.097 218.148 0.00 0.00
ATOM 5 HA2 GLYMX 2 78.666 155.314 219.365 0.00 0.00
ATOM 6 C GLYMX 2 79.990 156.626 220.263 0.00 0.00
ATOM 7 O GLYMX 2 79.711 156.407 221.481 0.00 0.00
ATOM 8 C1 GLYMX 2 77.237 157.357 217.950 0.00 0.00
ATOM 9 O1 GLYMX 2 76.377 158.234 218.053 0.00 0.00
ATOM 10 C2 GLYMX 2 77.036 156.296 216.900 0.00 0.00
ATOM 11 H2A GLYMX 2 76.607 155.361 217.327 0.00 0.00
ATOM 12 H2B GLYMX 2 78.031 156.193 216.427 0.00 0.00
ATOM 13 C3 GLYMX 2 76.099 156.709 215.763 0.00 0.00
ATOM 14 H3A GLYMX 2 76.557 157.515 215.157 0.00 0.00
ATOM 15 H3B GLYMX 2 75.115 156.979 216.205 0.00 0.00
ATOM 16 C4 GLYMX 2 75.840 155.554 214.747 0.00 0.00
ATOM 17 H4A GLYMX 2 75.493 154.710 215.386 0.00 0.00
ATOM 18 H4B GLYMX 2 76.864 155.330 214.410 0.00 0.00
ATOM 19 C5 GLYMX 2 74.827 155.829 213.672 0.00 0.00
ATOM 20 H5A GLYMX 2 74.956 156.819 213.193 0.00 0.00
ATOM 21 H5B GLYMX 2 73.834 155.996 214.145 0.00 0.00
ATOM 22 C6 GLYMX 2 74.848 154.569 212.748 0.00 0.00
ATOM 23 H6A GLYMX 2 74.831 153.679 213.406 0.00 0.00
ATOM 24 H6B GLYMX 2 75.778 154.592 212.133 0.00 0.00
ATOM 25 C7 GLYMX 2 73.606 154.438 211.773 0.00 0.00
ATOM 26 H7A GLYMX 2 72.602 154.400 212.250 0.00 0.00
ATOM 27 H7B GLYMX 2 73.751 153.466 211.261 0.00 0.00
ATOM 28 C8 GLYMX 2 73.665 155.414 210.621 0.00 0.00
ATOM 29 H8A GLYMX 2 74.294 154.967 209.812 0.00 0.00
ATOM 30 H8B GLYMX 2 74.188 156.339 210.943 0.00 0.00
ATOM 31 C9 GLYMX 2 72.286 155.753 210.036 0.00 0.00
ATOM 32 H9A GLYMX 2 72.573 156.201 209.052 0.00 0.00
ATOM 33 H9B GLYMX 2 71.819 156.579 210.602 0.00 0.00
ATOM 34 C10 GLYMX 2 71.378 154.517 209.840 0.00 0.00
ATOM 35 H10A GLYMX 2 71.105 154.068 210.820 0.00 0.00
ATOM 36 H10B GLYMX 2 71.823 153.612 209.385 0.00 0.00
ATOM 37 C11 GLYMX 2 70.009 154.921 209.242 0.00 0.00
ATOM 38 H11A GLYMX 2 69.550 154.079 208.672 0.00 0.00
ATOM 39 H11B GLYMX 2 70.301 155.636 208.429 0.00 0.00
ATOM 40 C12 GLYMX 2 68.986 155.407 210.230 0.00 0.00
ATOM 41 H12A GLYMX 2 69.540 156.184 210.790 0.00 0.00
ATOM 42 H12B GLYMX 2 68.789 154.689 211.048 0.00 0.00
ATOM 43 C13 GLYMX 2 67.776 156.083 209.725 0.00 0.00
ATOM 44 H13A GLYMX 2 68.080 156.991 209.154 0.00 0.00
ATOM 45 H13B GLYMX 2 67.141 156.584 210.487 0.00 0.00
ATOM 46 C14 GLYMX 2 66.864 155.200 208.842 0.00 0.00
ATOM 47 H14A GLYMX 2 66.097 155.906 208.456 0.00 0.00
ATOM 48 H14B GLYMX 2 67.443 154.827 207.957 0.00 0.00
ATOM 49 H14C GLYMX 2 66.382 154.367 209.397 0.00 0.00

GLYM residue is covalently linked to the protein. HN is defined in .rtp file as I have already provided in my last msg. What should be the reason I am getting this error by pdb2gmx?

Thanks.

Puja