[gmx-users] Fatal error with g_hbond

Grzegorz Jezierski jeziersk at bit.uni-bonn.de
Wed Mar 4 14:36:18 CET 2009


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
-------

Thank you for any hints
Grzegorz



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