[gmx-users] Re: hydrogen bonds

[Justin A. Lemkul]

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

========================================