Hi,<br><br>Just calculate the no. of atoms according to the choice of options and manually. you will understand why is it giving the error. Secondly check how gromacs calculate the no. of hydrogen bonds. It uses the cut-off 0.35 nm and 30 in version 3.3.1, but in earlier version the angle cut-off was 60 in version 3.2 and 120 in version 3.1.<br>
<br>regards<br>anil<br>IITB, India<br><br><div class="gmail_quote">On Mon, May 5, 2008 at 7:20 PM, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="Wj3C7c">Mark Abraham wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
sharada wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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>
g_hbond -f HBD1_15npep.trr -s HBD1_5mr_md.tpr -n HBD1_10n_nsl.ndx -num hnum.xvg -g hb.log<br>
<br>
this is the output I obtain and the hb.log file is not created :<br>
<br>
Reading file HBD1_5mr_md.tpr, VERSION 3.3 (single precision)<br>
Specify 2 groups to analyze:<br>
Group 0 ( Protein) has 358 elements<br>
Group 1 ( Protein-H) has 271 elements<br>
Group 2 ( C-alpha) has 36 elements<br>
Group 3 ( Backbone) has 108 elements<br>
Group 4 ( MainChain) has 144 elements<br>
Group 5 (MainChain+Cb) has 177 elements<br>
Group 6 ( MainChain+H) has 181 elements<br>
Group 7 ( SideChain) has 177 elements<br>
Group 8 ( SideChain-H) has 126 elements<br>
Group 9 ( Prot-Masses) has 358 elements<br>
Select a group: 3<br>
Selected 4: 'Backbone'<br>
Select a group: 3<br>
Selected 4: 'Backbone'<br>
Calculating hydrogen bonds in Backbone (108 atoms)<br>
Found 0 donors and 72 acceptors<br>
No Donors found<br>
</blockquote>
<br>
I haven't used this tool, but the problem looks like it is here. Are there any hydrogens in this group?<br>
</blockquote>
<br></div></div>
use 6<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Mark<br>
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<br>
<br></div><font color="#888888">
-- <br>
David van der Spoel, Ph.D.<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a></font><div>
<div></div><div class="Wj3C7c"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>(¨`•.•´¨) Always<br>`•.¸(¨`•.•´¨) Keep<br>(¨`•.•´¨)¸.•´ Smiling!<br>`•.¸.•´<br> «•´`•.(*•.¸(`•.¸ ¸.•´)¸.•*).•´`•» <br> «•´¨*•.¸¸. * ANIL *.¸¸.•*¨`•»<br> «•´`•.(¸.•´(¸.•* *•.¸)`•.¸).•´`•»<br>
<br>ANIL KUMAR(Research Scholar),<br>Bio-Organic Lab No-336(2nd Floor),<br>Dept. of Chemistry,I.I.T.Bombay,Powai,<br>Mumbai-400076,<br>Ph. No.-022-25764780(Lab)<br>Mobile:-09819638547<br>----------------------------------------- <br>
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