Hi everyone.
I want to analyze the hydrogen bonds between dppc carbonyl oxygen O22 and cholesterol hydroxyl group O3 H3. However, when I execute the gmx hbond command, it doesn't find the donor atoms.
I created the index file in the following way:
1 & a O3 | 1 & a H3 (donor, hydrogen)
0 & a O22
Thank you in advance.
I don't know your experience level, so I must ask - did you accidentally forget to use the -n flag for the H-bond analysis?
What was the output from gromacs when the command failed?
You could also do this in a less sensitive way (gmx hbond takes into account the angle) using gmx mindist using the two oxygen atoms as the groups you want to calculate the distance between.
Laura Pulido how about creating a group containing the three atoms and let gromacs decide the acceptors and the donors? then use this group in gmx hbond... hth!
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