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<TD>Hi, <br ><br >Thank you all for the response, Yes, the backbone of my protien does not have the required -Hydrogens for the program to calculate the hydrogen bonds. The option 6 (Mainchain +H) worked for me. Still I am not clear as to what exactly are cut off angle 30 degrees and cut-off radius .35 nm mean in the program g_hbond. Is it considering the hydrogen bond angle of 120 +/- 30 ? In that case cut-off angle 60 & 120 in other versions does not make sense ... Kindly clarify my doubts <br ><br >regards <br >sharada<br ><strong><em>-- Original Message --</em></strong><br >From: "Anil Kumar" <chemanil@gmail.com><br >To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br >Date: Mon, 5 May 2008 23:13:25 +0530<br >Subject: Re: [gmx-users] Angle definition in g_hbond ...<br ><br >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 TARGET="_blank" HREF="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</A>> wrote:<br ><blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote">
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<DIV CLASS="Wj3C7c">Mark Abraham wrote:<br > <blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote"> sharada wrote:<br > <blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote"> 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>
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<DIV CLASS="Ih2E3d"><br > <br > <blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote"> <br > Mark<br > _______________________________________________<br > gmx-users mailing list <A TARGET="_blank" HREF="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><br > <A TARGET="_blank" HREF="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><br > Please search the archive at <A TARGET="_blank" HREF="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!<br > Please don't post (un)subscribe requests to the list. Use the www interface or send it to <A TARGET="_blank" HREF="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<br > Can't post? Read <A TARGET="_blank" HREF="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><br > </blockquote> <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 TARGET="_blank" HREF="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</A> <A TARGET="_blank" HREF="mailto:spoel@gromacs.org">spoel@gromacs.org</A> <A TARGET="_blank" HREF="http://folding.bmc.uu.se">http://folding.bmc.uu.se</A></font>
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<DIV CLASS="Wj3C7c"><br > _______________________________________________<br > gmx-users mailing list <A TARGET="_blank" HREF="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><br > <A TARGET="_blank" HREF="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><br > Please search the archive at <A TARGET="_blank" HREF="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!<br > Please don't post (un)subscribe requests to the list. Use the www interface or send it to <A TARGET="_blank" HREF="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<br > Can't post? Read <A TARGET="_blank" HREF="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><br > </DIV>
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<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 > Residence:-<br >Hostel#1,Room#297,IIT Bombay,Powai,<br >Mumbai-400076,Ph.No.:-022-25721017(Hostel)<br >---------------------------------------------------------------------------<br > "Time is money and duty is God.....To rise in life , you must respect both !!!!!"<br > ---------------------------------------------------------------------------- _______________________________________________<br >gmx-users mailing list gmx-users@gromacs.org<br >http://www.gromacs.org/mailman/listinfo/gmx-users<br >Please search the archive at http://www.gromacs.org/search before posting!<br >Please don't post (un)subscribe requests to the list. Use the <br >www interface or send it to gmx-users-request@gromacs.org.<br >Can't post? Read http://www.gromacs.org/mailing_lists/users.php</TD>
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