Hi, 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.
regards anil IITB, India On Mon, May 5, 2008 at 7:20 PM, David van der Spoel <[EMAIL PROTECTED]> wrote: > Mark Abraham wrote: > >> sharada wrote: >> >>> dear gmx-users, >>> >>> 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. >>> >>> This is the command I am using: >>> >>> g_hbond -f HBD1_15npep.trr -s HBD1_5mr_md.tpr -n HBD1_10n_nsl.ndx -num >>> hnum.xvg -g hb.log >>> >>> this is the output I obtain and the hb.log file is not created : >>> >>> Reading file HBD1_5mr_md.tpr, VERSION 3.3 (single precision) >>> Specify 2 groups to analyze: >>> Group 0 ( Protein) has 358 elements >>> Group 1 ( Protein-H) has 271 elements >>> Group 2 ( C-alpha) has 36 elements >>> Group 3 ( Backbone) has 108 elements >>> Group 4 ( MainChain) has 144 elements >>> Group 5 (MainChain+Cb) has 177 elements >>> Group 6 ( MainChain+H) has 181 elements >>> Group 7 ( SideChain) has 177 elements >>> Group 8 ( SideChain-H) has 126 elements >>> Group 9 ( Prot-Masses) has 358 elements >>> Select a group: 3 >>> Selected 4: 'Backbone' >>> Select a group: 3 >>> Selected 4: 'Backbone' >>> Calculating hydrogen bonds in Backbone (108 atoms) >>> Found 0 donors and 72 acceptors >>> No Donors found >>> >> >> I haven't used this tool, but the problem looks like it is here. Are there >> any hydrogens in this group? >> > > use 6 > > >> Mark >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- (¨`•.•´¨) Always `•.¸(¨`•.•´¨) Keep (¨`•.•´¨)¸.•´ Smiling! `•.¸.•´ «•´`•.(*•.¸(`•.¸ ¸.•´)¸.•*).•´`•» «•´¨*•.¸¸. * ANIL *.¸¸.•*¨`•» «•´`•.(¸.•´(¸.•* *•.¸)`•.¸).•´`•» ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) Mobile:-09819638547 ----------------------------------------- Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-022-25721017(Hostel) --------------------------------------------------------------------------- "Time is money and duty is God.....To rise in life , you must respect both !!!!!" ----------------------------------------------------------------------------
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