[gmx-users] g_ hbond on two peptides

Erik Marklund erikm at xray.bmc.uu.se
Tue Jun 1 12:47:35 CEST 2010

Hsin-Lin Chiang skrev:
> Hi,
> I use g_hbond to analyze the system with two peptide.
> And I introduce the ndx file which include two group for the two 
> peptides respectively.
> For the first prompt of g_hbond, I choose the group of the first peptide.
> For the second prompt, I choose the other peptide.
> I got the data that announced 4 H-bonds were found.
> And then I use rasmol to check, I found there are 2 intra-H-bonds in 
> first peptide and 2 intra-H-bonds in the second.
> There are no inter-H-bonds between two peptides in my system.
> It's strange since I had selected different group to analyze when 
> g_hbond promted.
> How should I do to exclude the intra-H-bond on one peptide?
> Hsin-Lin
That sounds strange indeed. Have you looked into which hbonds are found? 
And are you sure your index file is error free?


Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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