[gmx-users] Hydrogen bonds between new residue and protein.

Dawid das addiw7 at googlemail.com
Wed Aug 20 18:02:27 CEST 2014

I found one problem. If I create new group in index.ndx file which contains
protein without CH6 residue then some h-bonds are detected but actually I
wouldn't expect it the way it looks.

So again, how does actually g_hbond calculate hydrogen bonds except the
distance and angle restraints. Does it recognize donors and acceptors by
the atom types? If so, how can I force it to recognize MO3 as h-bond
acceptor for instance?

2014-08-20 16:44 GMT+01:00 Dawid das <addiw7 at googlemail.com>:

> Dear Gromacs experts,
> This time I would like to use g_hbond to calculate hydrogen bonds between
> one residue of the protein and all other residues in the protein. The thing
> is that the former residue is a new one, defined by me from scratch. Now
> when I run g_hbond and choose CH6 and Protein index groups (CH6 is my new
> residue and Protein also includes this CH6 residue) I got 0.0 for every
> time step although I strongly believe there are couple of hydrogen bonds.
> I was thinking that the issue may be that CH6 is built of atomtypes which
> are not recognised by g_hbond as ones able to form hydrogen bonds. Is it
> possible explanation? If yes, what can I do? Is recompiling what I need to
> do?
> Thanks,
> Dawid Grabarek

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