<DIV>Hello,</DIV>
<DIV> </DIV>
<DIV>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. </DIV>
<DIV>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.</DIV>
<DIV> </DIV>
<DIV>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?</DIV>
<DIV> </DIV>
<DIV>Thanks in advance,</DIV>
<DIV>Maarten Wolf </DIV><p>
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