[gmx-users] ffamber99p -- .hdb editing

[Stas Bobritsky]

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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