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> >>>>> <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/** >>>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>>>> posting! >>>>> >>>>> * Please don't post (un)subscribe requests to the list. Use the >>>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>>> * Can't post? 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