[gmx-users] Re: hydrogen bonds

[Vasilis Georgilas]

sorry for keep spamming you...

so i make 2 groups: acceptors and donors (with their hydrogen)

I hope now i am correct!


On Sat, Jul 31, 2010 at 1:55 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Vasilis Georgilas wrote:
>
>> I didn't get why the command i propsed won't work.
>>
>>
> Because you typed:
>
> a HO a OM a O
>
> I assumed you meant you would actually try this with make_ndx.  It is wrong
> for several reasons, the most immediate of which is the use of "a" with atom
> types.  To use "a" you must supply atom *names* not types.  If you want to
> specify any selections based on types, you must provide a .tpr file as input
> and use "t" instead of "a."
>
>
>  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
>>
>>
> These groups sound almost correct, but they do not correspond to what you
> typed before.  You can't specify the hydrogen as its own group, since it
> won't be connected to its donor atom (O4).  To specify the hydroxyl, for
> example, what you want is:
>
> a H2 | a O4
>
> -Justin
>
>  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<mailto:
>> 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 <http://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 <mailto:vasilis.georgilas at BEST.eu.org
>> >
>> mobile: +306973041057
>>
>
> --
> ========================================
>
> 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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