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
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-----------------------------------------------
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
[email protected] http://folding.bmc.uu.se/
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