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

Justin Lemkul jalemkul at vt.edu
Wed Aug 20 19:14:04 CEST 2014

On 8/20/14, 12:02 PM, Dawid das wrote:
> 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?

It reads the first character of atom names, nothing more.  The best bet is to 
name atoms more conventionally, such that the first letter is the actual 
elemental symbol.  You can do this after the simulation by editing the .top and 
producing a new .tpr file with new names.  It doesn't affect the simulation in 
any way.


> 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


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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