<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>dear gmx-users,<br ><br >I have a very fundamental query. I am trying to obtain the backbone hydrogen bonds formed during a 15ns simulation of a 35 long protein. When I do this by using g_hbond and selecting the Backbone groups, I am getting no hydrogen bonds at all . However, when I plot the hydrogen bonds for some of the structures picked up through the dynamics using InsightII I am able to see the backbone HBs in almost all of them. <br ><br >This is the command I am using: <br ><br > <SPAN STYLE="font-style: italic;">g_hbond -f HBD1_15npep.trr -s HBD1_5mr_md.tpr -n HBD1_10n_nsl.ndx -num hnum.xvg -g hb.log</SPAN><br style="font-style: italic;" ><br >this is the output I obtain and the hb.log file is not created :<br ><br ><SPAN STYLE="font-weight: bold;">Reading file HBD1_5mr_md.tpr, VERSION 3.3 (single precision)</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Specify 2 groups to analyze:</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Group 0 ( Protein) has 358 elements</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Group 1 ( Protein-H) has 271 elements</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Group 2 ( C-alpha) has 36 elements</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Group 3 ( Backbone) has 108 elements</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Group 4 ( MainChain) has 144 elements</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Group 5 (MainChain+Cb) has 177 elements</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Group 6 ( MainChain+H) has 181 elements</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Group 7 ( SideChain) has 177 elements</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Group 8 ( SideChain-H) has 126 elements</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Group 9 ( Prot-Masses) has 358 elements</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Select a group: 3</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Selected 4: 'Backbone'</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Select a group: 3</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Selected 4: 'Backbone'</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Calculating hydrogen bonds in Backbone (108 atoms)</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Found 0 donors and 72 acceptors</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">No Donors found</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">-------------------------------------------------------</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Program g_hbond, VERSION 3.3</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Source code file: gmx_hbond.c, line: 1827</SPAN><br style="font-weight: bold;" ><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Fatal error:</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Nothing to be done</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">-------------------------------------------------------</SPAN><br style="font-weight: bold;" ><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">"Keep Your Shoes and Socks On, People" (F. Zappa)</SPAN><br style="font-weight: bold;" ><br > Could anyone please let me know the distance and angle definition used in the program g_hbond. There is a mention about cutoff angle and Cutoff radius as shown below. <br ><br > <SPAN STYLE="font-style: italic;">-a real 30 Cutoff angle (degrees, Donor - Hydrogen -</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> Acceptor)</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> -r real 0.35 Cutoff radius (nm, X - Acceptor, see next option)</SPAN><br style="font-style: italic;" ><br >What exactly is the Cutoff angle ? Usually the angle of Donor - Hydrogen -Acceptor is around 120 degrees and the distance is around 0.2nm. I have searched the gromacs forum but could not get any help. thanks for your patience reading. <br ><br >sharada</BODY></HTML>