[gmx-users] adding missing hydrogen in PDB files

[Justin A. Lemkul]

Indeed, there are .hdb entries for nucleic acids in the Amber ports.  I wasn't
sure, but grepped for the wrong thing, so yes, they're there!

Sorry for the mistake.

-Justin

Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:

> 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
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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