[gmx-users] ffamber99p -- .hdb editing

[Yang Ye]

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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