[gmx-users] Hydrogen bonding differences

[Erik Marklund]

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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