[gmx-users] Hydrogen bonding differences

[Kavyashree M]

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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