[gmx-users] Triple helix built by THeBuScr can not transform by pdb2gmx in Gromacs

[Ming Tang]

Dear all,
I built an triple helix using the THeBuScr, and used pdb2gmx (with -ignh)  to get the .top file in GROMACS. But it emerged fatal error:
Atom CD in residue HYP 12 was not found in rtp entry HYP with 15 atoms while sorting atoms.
I have tried every kind of force field but those including HYP residual emerged the same error.

Atoms in triple helix pdb file:
ATOM     86  N   HYP A  12      30.850  -3.083   2.256  1.00  0.00           N
ATOM     87  CA  HYP A  12      32.080  -2.296   2.141  1.00  0.00           C
ATOM     88  C   HYP A  12      32.710  -2.496   0.763  1.00  0.00           C
ATOM     89  O   HYP A  12      32.550  -3.518   0.123  1.00  0.00           O
ATOM     90  CB  HYP A  12      32.970  -2.847   3.254  1.00  0.00           C
ATOM     91  CG  HYP A  12      32.015  -3.467   4.236  1.00  0.00           C
ATOM     92  CD  HYP A  12      30.918  -4.039   3.374  1.00  0.00           C
ATOM     93  OD  HYP A  12      31.492  -2.476   5.095  1.00  0.00           O

Atoms in amber03 aminoacids.tpr
[ HYP ] ;
[ atoms ]
     N    N           -0.25480     1
   CD2    CT           0.05950     2
  HD21    H1           0.07000     3
  HD22    H1           0.07000     4
    CG    CT           0.04000     5
    HG    H1           0.04160     6
   OD1    OH          -0.61340     7
   HD1    HO           0.38510     8
    CB    CT           0.02030     9
   HB1    HC           0.04260    10
   HB2    HC           0.04260    11
    CA    CT           0.00470    12
    HA    H1           0.07700    13
     C    C            0.58960    14
     O    O           -0.57480    15
When ignoring H, the heavy atoms in HYP residual match well between the pdb file and the aminoacids.tpr

I have got stuck here for almost one months, and hope somebody can give me some advices and solutions.
Thanks very much