[gmx-users] Re: hydrogen bonds

[Justin A. Lemkul]

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

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