Thank you Sir for clarifying the confusion. Regards kavya
On Fri, Mar 22, 2013 at 11:18 PM, Erik Marklund <er...@xray.bmc.uu.se>wrote: > I wouldn't say wrong, but I realized that some residue may make two hbonds > to different parts of the protein, i.e. to the main chain and to a side > chain at the same time. With -merge this counts as one if you analyze the > entire protein. If you split your analysis such hbonds will show up in both > e.g. SS and MS, hence TOT < MM+SS+MS. It's just another way of counting > hbonds. > > Erik > > > On Mar 22, 2013, at 5:32 PM, Kavyashree M wrote: > > Sir, >> >> I tried -nomerge. It is fine now. But will it be wrong to >> calculate without nomerge option? >> >> Thank you >> Kavya >> >> On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund <er...@xray.bmc.uu.se> >> wrote: >> >> I could see how -merge (on by default) could lead to this. Have you tried >>> -nomerge? >>> >>> Erik >>> >>> >>> On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote: >>> >>> Dear Users, >>> >>>> >>>> As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds. >>>> Still the >>>> Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen >>>> bond. >>>> Is there any other solution? >>>> >>>> Thank you >>>> Kavya >>>> >>>> On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M <hmkv...@gmail.com> >>>> wrote: >>>> >>>> Dear Sir, >>>> >>>>> >>>>> Sure I will try with 4.6. presently I am not able to download it. >>>>> >>>>> Thank you >>>>> kavya >>>>> >>>>> >>>>> On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund <er...@xray.bmc.uu.se >>>>> >>>>>> wrote: >>>>>> >>>>> >>>>> There were a handful of bugfixes to g_hbond over the last year. Could >>>>> >>>>>> you >>>>>> try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form >>>>>> before. >>>>>> >>>>>> Erik >>>>>> >>>>>> >>>>>> On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote: >>>>>> >>>>>> Dear Sir, >>>>>> >>>>>> >>>>>>> This is 4.5.3. I have not tried nomerge. I did not use >>>>>>> nomerge option in any of them, So if it has counted >>>>>>> it (Hbond b/w same donor and acceptor but with >>>>>>> different hydrogen) twice in one calculation then it will >>>>>>> be counted twice in another, So wont the result with/without >>>>>>> nomerge be the same? >>>>>>> >>>>>>> The difference is 4-5 Hbonds.. >>>>>>> >>>>>>> Thank you >>>>>>> Kavya >>>>>>> >>>>>>> On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund <er...@xray.bmc.uu.se >>>>>>> > >>>>>>> wrote: >>>>>>> >>>>>>> Hi. What version was this? Have you tried with -nomerge? >>>>>>> >>>>>>> >>>>>>>> Erik >>>>>>>> >>>>>>>> >>>>>>>> On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: >>>>>>>> >>>>>>>> Dear users, >>>>>>>> >>>>>>>> >>>>>>>> While calculating hydrogen bonds for a simulation, it >>>>>>>>> was found that the average number of intra protein >>>>>>>>> hbonds was not equal to sum of MM, MS and SS >>>>>>>>> hydrogen bonds. (MM - main chain - main chain, >>>>>>>>> MS - main chain - side chain and side chain - side >>>>>>>>> chain hydrogen bonds). There was a difference of 5 >>>>>>>>> or so hbonds between intra-protein and MM+MS+SS >>>>>>>>> hbonds. why is this so? >>>>>>>>> I selected the options 7 7 for MM, 7 8 for MS and 8 8 >>>>>>>>> for SS hydrogen bonds. >>>>>>>>> >>>>>>>>> One clarification. nhbdist option gives 0, 1, 2, 3 and >>>>>>>>> total hydrogen bonds per hydrogen. Does this mean >>>>>>>>> that a single hydrogen involving in forming hbond with >>>>>>>>> 2 different acceptors/donors at different points of time >>>>>>>>> in the trajectory. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> kavya >>>>>>>>> -- gmx-users mailing list gmx-users@gromacs.org >>>>>>>>> http://lists.gromacs.org/********mailman/listinfo/gmx-users<http://lists.gromacs.org/******mailman/listinfo/gmx-users> >>>>>>>>> <ht**tp://lists.gromacs.org/******mailman/listinfo/gmx-users<http://lists.gromacs.org/****mailman/listinfo/gmx-users> >>>>>>>>> > >>>>>>>>> <htt**p://lists.gromacs.org/******mailman/listinfo/gmx-users<http://lists.gromacs.org/****mailman/listinfo/gmx-users> >>>>>>>>> <h**ttp://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>>>>>> > >>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> <htt**p://lists.gromacs.org/****mailman/**listinfo/gmx-users<http://lists.gromacs.org/**mailman/**listinfo/gmx-users> >>>>>>>>> <h**ttp://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users> >>>>>>>>> > >>>>>>>>> <h**ttp://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>>>>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>>>>>> > >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> * Please search the archive at http://www.gromacs.org/** >>>>>>>>>> >>>>>>>>> Support/Mailing_Lists/Search<****h**ttp://www.gromacs.org/**** >>>>>>>>> Support/** <http://www.gromacs.org/**Support/**>< >>>>>>>>> http://www.gromacs.**org/Support/**<http://www.gromacs.org/Support/**> >>>>>>>>> > >>>>>>>>> >>>>>>>>> Mailing_Lists/Search<http://****www.gromacs.org/Support/**<http://www.gromacs.org/Support/**> >>>>>>>>> >>>>>>>>> Mailing_Lists/Search<http://**www.gromacs.org/Support/** >>>>>>>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search> >>>>>>>>> > >>>>>>>>> >>>>>>>>>> before >>>>>>>>>>> >>>>>>>>>> posting! >>>>>>>>> >>>>>>>>> * Please don't post (un)subscribe requests to the list. 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