[gmx-users] Re: hydrogen bonds

[Vasilis Georgilas]

I didn't get why the command i propsed won't work.

My idea, according what you proposed, is to use make_ndx and then make 3
groups:

oxygen with the doble bond, oxyegn of carboxyle and hydroxele

and then with the g_hbond to do all the calculations.

Right??

thank you once again for the help

On Fri, Jul 30, 2010 at 8:19 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Vasilis Georgilas wrote:
>
>> This is from my topology file for palmitic acid.
>>
>> You say a should make a group of all O, of OM and of HO.
>>
>> But for the calculation I need the angle between hydrogene - donor -
>> acceptor.
>> So my index file should be in triplets, right?? this means I should type a
>> HO a OA a O.
>>
>> Correct?
>>
>>
> No.  The donor and acceptor groups should be separate.  The geometry is
> easily calculated from O-H...O coordinates.  You should also not have a
> group for just hydrogen, you need the group to contain the relevant
> functional group, which is the hydroxyl in this case (atoms H2 and O4 in a
> single group).
>
> Also note that your proposed command will not work.  To select by atom type
> (i.e., HO, OA, and O) you need to provide a .tpr file as input to make_ndx
> and use "t HO" etc.  Otherwise, select by atom name.
>
> -Justin
>
>
>  thank you
>>
>>
>> [ atoms ]
>> ;   nr    type   resnr  residu    atom    cgnr        charge       1
>>  HO       1    PLM     H2        1     0.370             2      OM       1
>>  PLM     O4        1    -0.460            3       C       1    PLM     C3
>>      1     0.42             4       O       1    PLM     O5        1
>>  -0.45             5     CP2       1    PLM     C4        2     0.12
>>   6     CP2       1    PLM     C5        3     0           7     CP2       1
>>    PLM     C6        4     0        8     CP2       1    PLM     C7        5
>>     0
>>     9     CP2       1    PLM     C8        6     0
>>    10     CP2       1    PLM     C9        7     0
>>    11     CP2       1    PLM     C10       8     0
>>    12     CP2       1    PLM     C11       9     0
>>    13     CP2       1    PLM     C12      10     0
>>    14     CP2       1    PLM     C13      11     0
>>    15     CP2       1    PLM     C14      12     0
>>    16     CP2       1    PLM     C15      13     0
>>    17     CP2       1    PLM     C16      14     0
>>    18     CP2       1    PLM     C17      15     0
>>    19     CP3       1    PLM     C18      16     0
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
Vasilis Georgilas
LBG Patra
Joint EoE Brno Coordinator
mail: vasilis.georgilas at BEST.eu.org
mobile: +306973041057
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