[gmx-users] ffamber99p -- .hdb editing

[Mark Abraham]

Stas Bobritsky wrote:

> 
> 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?

Chapter five in the manual.

Mark