[gmx-users] g_ hbond on two peptides

[Erik Marklund]

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

-- 
-----------------------------------------------
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/