[gmx-users] Problems with g_hbond

[Ran Friedman]

Hi Rolf,
Try renaming the atom names to something that starts with O and H for
oxygen and hydrogen.
Good luck,
Ran.

Rolf Erwin Isele-Holder wrote:
> Dear users,
>
> I'm running a simulation which uses ethanol as solvent. When using g_hbond the programm is able to recognize the solute's donors and acceptors, however it does not recognize any acceptors or donors of ethanol. Here is a part of my topology:
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
>      1         HO      1   ETHH     EH      1      0.398      1.008   ; qtot 0.398
>      2         OA      1   ETHH     EO      1     -0.548    15.9994   ; qtot -0.15
>      3        CH2      1   ETHH    EC1      1       0.15     14.027   ; qtot 0
>      4        CH3      1   ETHH    EC2      2          0     15.035   ; qtot 0
>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     1 
>     2     3     1 
>     3     4     1 
>
> Why doesn't g_hbond recognize any donors or acceptors?
>
> Regards,
>
> Rolf
>