[gmx-users] adding missing hydrogen in PDB files

[Vigneshwar Ramakrishnan]

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.

Thank you,
Vignesh

On Fri, May 2, 2008 at 12:09 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
> In terms of external software, check out OpenBabel:
> http://openbabel.org/wiki/Main_Page
>
> There's also the H++ server, which employs Babel as part of its algorithm:
> http://biophysics.cs.vt.edu/H++/index.php
>
> I believe H++ can handle nucleic acids.  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.
>
> -Justin
>
> Quoting Arijit Maitra <arijitmaitra at yahoo.com>:
>
> > Hi All
> >
> > I have been trying to simulate a DNA tetramer
> > d(GGGGTTTTGGGG)_2 using gromacs with amber ports. I
> > have downloaded the X-ray structure from
> > www.rcsb.org/pdb which has several missing hydrogen
> > atoms. Can anybody advise how to plug in the missing
> > atoms, e.g. with softwares or otherwise to proceed
> > with the pdb2gmx command?
> >
> > Thanks
> > Ari
> >
> >
> >
> >
>
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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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-- 
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

"The rewards of sincere resolves are highs money can never buy!"
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