[gmx-users] hydrogen bonds of peptide with lipids

[Justin A. Lemkul]

Quoting maria goranovic <mariagoranovic at gmail.com>:

> Yes, I looked into that. But could not find any information about how to
> include new acceptor or donor atoms. Could you please be more specific ?
> Thank you !

These are probably defined in the source code, but I'll admit that I have never
gone looking for them.  You could modify the code, but I'd hate to think that
you'd have to recompile each time you want to analyze a different system :-)

Aside to the developers: Maybe interactive selection of atom types for H-bond
analysis could be a future feature?

-Justin

>
> On Thu, Apr 17, 2008 at 12:34 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> > Quoting maria goranovic <mariagoranovic at gmail.com>:
> >
> > > Dear All,
> > >
> > > Where are the donor and acceptor atoms defined for the g_hbond analysis
> > ? I
> > > was trying to calculate h-bonds between a peptide and a popc bilayer,
> > but
> > > there are no acceptor or donors listed for POPC. How can one change this
> > ?
> >
> > Have a look at g_hbond -h
> >
> > -Justin
> >
> > >
> > > Sincerely,
> > > -Maria
> > >
> > > --
> > > Maria G.
> > > Technical University of Denmark
> > > Copenhagen
> > >
> >
> >
> >
> > ========================================
> >
> > 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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>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>



========================================

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/

========================================