Hi, Erik and XAvier
Thank you for your help
I have had a idea to check my data.
I selected the "protein" group two times and I get 5 H-bonds.
Then I select first and second peptide group two time and get 0 and 1
H-bond respectively.
And 5 minus 1 is equal to 4 that is equal to the number of H-bonds in my
last message.
So I think maybe it's just because the manners of two programs are
different.
regards,
Hsin-Lin
> 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
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