I suggest you may find solution outside Gromacs. Use Pymol or other software to simply add hydrogen. Check it (usually they will ignore some double bonds) and put it back to GROMACS.

Regards,
Yang Ye

On 4/23/2007 5:24 PM, Stas Bobritsky wrote:
Hi all!

I`m working on tRNA MD. My structure contains modified base 2MG, which have been added to the ffamber99p.rtp:

[2MG]
 [atoms]
    P     amber99_46    1.08783    1
    O1P   amber99_45   -0.76666     2
    O2P   amber99_45   -0.76666    3
    O5'   amber99_44   -0.47131    4
    C5'   amber99_11    0.06353    5
    H5'1  amber99_19    0.06892    6
    H5'2  amber99_19    0.06892    7
    C4'   amber99_11    0.03859    8
    O4'   amber99_44   -0.32723    9
    C1'   amber99_11    0.04596    10
    C2'   amber99_11    0.07745    11
    O2'   amber99_43   -0.59135    12
    HO'2  amber99_25    0.41014    13
    H2'   amber99_19    0.09290    14
    N9    amber99_40   -0.00919    15
    C8    amber99_6     0.10447    16
    N7    amber99_36   -0.55207    17
    C5    amber99_4     0.13484    18
    C6    amber99_2     0.58227    19
    O6    amber99_41   -0.55183    20
    N1    amber99_35   -0.60808    21
    C2    amber99_3     0.65874    22
    N2    amber99_38   -0.55992    23
    H21   amber99_17    0.35843    24
    C10   amber99_11   -0.07537    25
    H20   amber99_19    0.08216    26
    H21   amber99_19    0.08216    27
    H22   amber99_19    0.08216    28
    N3    amber99_37   - 0.54563    29
    C4    amber99_4     0.19346    30
    H1    amber99_17    0.34611    31
    H8    amber99_24    0.15910    32
    H1'   amber99_20    0.16432    33
    H4'   amber99_19    0.11682     34
    C3'   amber99_11    0.21246    35
    H3'   amber99_19    0.08253    36
    O3'   amber99_44   -0.48898    37

 [bonds]
...
...

After pdb2gmx -f trna.pdb -o trna.gro -v  Gromacs says:

WARNING: atom H5'1 is missing in residue 2MG 1 in the pdb file
You might need to add atom H5'1 to the hydrogen database of residue 2MG
         in the file ff???.hdb (see the manual)
WARNING: atom H5'2 is missing in residue 2MG 1 in the pdb file
You might need to add atom H5'2 to the hydrogen database of residue 2MG
         in the file ff???.hdb (see the manual)
...
...
I try to study hdb file by comparing .rtp, .pdb, and .hdb- entries, but my PDB structure does not contain any H-atoms.
Where can I read about .hdb entry format for AMBER forcefield?
------------------------------------------------------------------------

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