[gmx-users] g_ hbond on two peptides

[XAvier Periole]

On Jun 1, 2010, at 12:47 PM, Erik Marklund wrote:

> 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?
You may also want to check that both programs define H-bond in
the same manner.
>
> /Erik
>
> -- 
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
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> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>
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