[gmx-users] Fatal error with g_hbond

[Justin A. Lemkul]

Grzegorz Jezierski wrote:
> Hello Gromacs users,
> I want to calculate hydrogen bonds over the trajectory, but only H-bonds 
> formed by a specific solute atom and any of the solvent molecules.
> I typed the following command:
> g_hbond -f md.trr -s md.tpr -n index.ndx -num hbnum -g hbond
> and the index file specified contains the atom of interest (in group 3) 
> and all the water hydrogens (group 10):
> -------
> [ oxygen ]
> 556
> [ solvent-O ]
> 6401 6404 6407 6410 6413 6416 6419 6422 6425 6428 6431 6434 6437 6440 
> 6443 6446 6449 6452 6455 6458
> (...)   <<-- long list
> -------
> 
> but what I get is this output:
> -------
> Specify 2 groups to analyze:
> Group     0 (  phosphorus) has     1 elements
> Group     1 (      carbon) has     1 elements
> Group     2 (    nitrogen) has     1 elements
> Group     3 (      oxygen) has     1 elements
> Group     4 (       water) has     3 elements
> Group     5 (         N-O) has     2 elements
> Group     6 (   nitrogens) has   128 elements
> Group     7 (      P8-C13) has     2 elements
> Group     8 (  P8-C13-all) has   256 elements
> Group     9 (      lipid1) has    50 elements
> Group    10 (   solvent-O) has  3655 elements
> Select a group: 3
> Selected 3: 'oxygen'
> Select a group: 10
> Selected 10: 'solvent-O'
> Checking for overlap in atoms between oxygen and solvent-O
> Calculating hydrogen bonds between oxygen (1 atoms) and solvent-O (3655 
> atoms)
> Found 0 donors and 3655 acceptors
> No Donors found
> Program g_hbond, VERSION 3.3.3
> Source code file: gmx_hbond.c, line: 1911
> Fatal error:
> Nothing to be done
> -------
> 

The groups must include the H atoms involved as well, since technically there is 
no H-bond between two oxygens.

-Justin

> Thank you for any hints
> Grzegorz
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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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