[gmx-users] adding missing hydrogen in PDB files

[Arijit Maitra]

Thanks everybody for the help. I updated the relevant
.hdb file after following the manual but one needs
some knowledge about the chemical structure of the DNA
(or this can be figured out from the bond information)
and the way indices have been used in the .pdb file
for the different atoms. This seems to work.

Ari 

--- "Justin A. Lemkul" <jalemkul at vt.edu> wrote:

> 
> 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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