[gmx-users] Hydrogen bonding differences

Sat Mar 23 05:47:55 CET 2013

Thank you Sir for clarifying the confusion.

Regards
kavya

On Fri, Mar 22, 2013 at 11:18 PM, Erik Marklund <erikm at 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 <erikm at 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 <hmkvsri at 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 <erikm at 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 <erikm at 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
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