"No default Bond types" error during grompp for specbond.dat bonds

shahina
Wed, 29 Jan 2025 08:36:08 +0000
User discussions

GROMACS version: 2023.3
GROMACS modification: No

I have tried to create a non-natural amino acid for incorporation into a peptide backbone. The non-natural amino acid is essentially a cysteine with an attached benzene for thioether stapling to the next cysteine (stapling of protein residues). The coordinates for my new residue CBZ are as follows:

ATOM      1  N   CBZ A   1       9.319   2.057  -8.838  1.00  0.00           N
ATOM      2  CA  CBZ A   1      10.697   2.451  -8.554  1.00  0.00           C
ATOM      3  C   CBZ A   1      11.649   1.852  -9.563  1.00  0.00           C
ATOM      4  O   CBZ A   1      12.529   2.527 -10.117  1.00  0.00           O
ATOM      5  CB  CBZ A   1      11.036   2.040  -7.109  1.00  0.00           C
ATOM      6  SG  CBZ A   1      12.554   1.510  -6.288  1.00  0.00           S
ATOM      7  CD  CBZ A   1      13.979   1.550  -7.325  0.00  0.00           C
ATOM      8  CE1 CBZ A   1      14.259   0.402  -8.085  0.00  0.00           C
ATOM      9  CE2 CBZ A   1      14.771   2.701  -7.472  0.00  0.00           C
ATOM     10  CZ1 CBZ A   1      15.331   0.405  -8.992  0.00  0.00           C
ATOM     11  CZ2 CBZ A   1      15.843   2.703  -8.380  0.00  0.00           C
ATOM     12  CH  CBZ A   1      16.124   1.556  -9.140  0.00  0.00           C
CONECT    1    2
CONECT    2    1    3    5
CONECT    3    2    4
CONECT    4    3
CONECT    5    2    6
CONECT    6    5    7
CONECT    7    6    8    9
CONECT    8    7   10
CONECT    9    7   11
CONECT   10    8   12
CONECT   11    9   12
CONECT   12   10   11
END

I want to link CBZ’s CH to CYS’s SG.

I have generated parameters from CGenFF and copied everything into charmm36.ff force field files (aminoacids.rtp, aminoacids.hdb, specbond.dat, residuetypes.dat, ffbonded.itp), taking care to keep naming parameters consistent. There are no issues during pdb2gmx and the special bonds are formed as described.

Despite everything, during the grompp step, gmx grompp is unable to recognize the special bonds and is asking for default bond parameters. The errors are as follows:

ERROR 1 [file file.top, line 532]:
No default Bond types

ERROR 2 [file file.top, line 640]:
No default Bond types

The entries in ffbonded.itp are as follows:

; bond parameters from CBZ.str
;      i        j  func           b0           kb
       S       CA     1   0.17500000    234304.00
      CA        S     1   0.17500000    234304.00

I am also getting errors for “No default U-B types” and “No default Proper Dih. types”. I have tried finding analogous entries for my atoms and added them as well.

I don’t understand why it is not working. Please help.

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