[gmx-users] g_hbond, problems mapping h-bonds

Maarten Wolf maarten_wolf at yahoo.co.uk
Wed Sep 29 07:21:23 CEST 2004

Sorry, forgot the subject.
I have calculated a 10 ns trajectory of a small protein dissolved in SPC water. Now I am interested in all the hydrogen bonds between the different residues inside the protein. I have tried to use g_hbond to calculate this, but I am only able to calculate the number of hydrogen bonds. 
If I use the contact map option -hbm I get a segmentation fault. If I try to print the hydrogen bond triplets in an index file, it writes only the possible donors and acceptors, but not the actual donor-acceptor pairs formed in the system. I used Gromacs version 3.2.1.
Does anybody know another way to map the hydrogen bonds formed within the protein? Does anybody know or has suggestions why the two methods I tried do not work?
Thanks in advance,
Maarten Wolf 

Groetjes Maarten

Luxemburglaan 7
1946 SB Beverwijk
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