[gmx-users] Re: g_ hbond on two peptides

[Hsin-Lin Chiang]

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
>>