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

Dawid das addiw7 at googlemail.com
Wed Aug 20 17:44:32 CEST 2014

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


Dawid Grabarek

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