[gmx-users] nucleic acid PDB input files

[Cameron Mura]

Hi,
Would anyone who's successfully used "pdb2gmx" to convert a DNA or RNA 
starting structure in PDB format to Gromacs format please send me a 
sample of their input PDB file?? I'd greatly appreciate it, as I can't 
seem to get beyond errors of this sort when running pdb2gmx:

> ...
> ...
> Making bonds...
>
> WARNING: atom H21 is missing in residue DGUA 1 in the pdb file
>          You might need to add atom H21 to the hydrogen database of 
> residue DGUA
>          in the file ff???.hdb (see the manual)
>
> WARNING: atom H22 is missing in residue DGUA 1 in the pdb file
>          You might need to add atom H22 to the hydrogen database of 
> residue DGUA
>          in the file ff???.hdb (see the manual)
>
> WARNING: atom H1 is missing in residue DGUA 1 in the pdb file
>          You might need to add atom H1 to the hydrogen database of 
> residue DGUA
>          in the file ff???.hdb (see the manual)
>
> Fatal error: There were 3 missing atoms in molecule Protein, if you 
> want to use this incomplete topology anyhow, use the option -missing


Thanks,
Cameron