[gmx-users] g_hbond in/output

Erik Marklund erikm at xray.bmc.uu.se
Wed Dec 20 23:50:31 CET 2006

20 dec 2006 kl. 17.34 skrev OZGE ENGIN:

> Hi,
> I have some questions about g_hbond option.
> 1) My system consists of a protein molecule (a capped 1 alanine  
> residue) (CH3-CO-ALA-NH-CH3) and 250 water molecules. After  
> selecting the g_hbond option, it says that protein molecule  
> consists of 12 elements; however, it consists much more elements as  
> it can be seen. Could you explain the reason behind it?
It depends. Are you using a united atoms force field? If not, have  
you had a look on which atoms are really part of the group "protein"?  
It might be the case that the caps are not recognized as Protein. You  
should probably make an index file with a index group specifying  
exactly which atoms are part of your molecule and use the -n option  
in g_hbond.
> 2) In order to investigate the Hydrogen bonds formed between water  
> molecules and the protein, should I select the protein and solvent  
> option? I selected like this, but I encountered with the following  
> error:
> Range checking error:
> Variable gx has value -3. It should have been within [ 0 .. 5 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
Hm. Don't know right away. Have to get back to you on that one.
> 3) In the output file of hbnum.xvg, there are three columns.I  
> think, the first column represents the time step, the second column  
> the number of hydrogen bonds. What about the third column?
That would be interactions fulfilling the distance criterion for h- 
bonds (default is within 3.5 Å) but not the HDA angle criterion. This  
can be seen in the header of the xvg-file (if one knows the file  
format), or in the legend if one views the file in e.g. (xm)grace.
> Thanks in advance
> Özge ENGİN
> Department of Computational Science and Engineering
> Koc University, Istanbul
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/Erik Marklund

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