[gmx-users] adding missing hydrogen in PDB files

[Mark Abraham]

Vigneshwar Ramakrishnan wrote:
> Hi All,
>  
> I am a newbie to GROMACS, so pardon me if I am wrong.
>  
> I think pdb2gmx can handle this with amber forcefields. We just need to 
> use the right nomenclature. I think the .hdb files for amber ff in 
> GROMACS are already equipped with the necessary info.
>  
> I am not sure why one must use an external software for adding the 
> hydrogen atoms.
>  
> If I am wrong, pls correct me.

No you're both (potentially) right.

> On Fri, May 2, 2008 at 12:09 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>  You could also do all of
>     this with
>     Gromacs, if you can come up with relevant entries in the .hdb file
>     for your
>     particular force field.  Then pdb2gmx could produce the right
>     structure with
>     added hydrogens.

If the port of the AMBER force fields to GROMACS have suitable .hdb 
files, then pdb2gmx can deal with the problem.

Mark