[gmx-users] Problems with g_hbond

[Mark Abraham]

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?

See g_hbond -h. The recognition is based on the atom name, and this 
conventionally doesn't start with E, as in your case. You will need to 
change the atom names in your initial coordinate file and topology, 
regenerate your .tpr, and then attempt the analysis. The trajectory is 
fine, since it has no atom names. Just keep the atom order the same!

Mark