[gmx-users] Hydrogen bond existence map

Nidhi Katyal nidhikatyal1989 at gmail.com
Thu Jun 19 11:48:23 CEST 2014

Hi all

I would like to create hydrogen bond existence map for interaction of each
residue with my ligand. I am aware that -hbm and -hbn option of g_hbond
along with index file would serve the purpose. But the resulting output
file is giving existence map for each atom of the residue. Instead, I want
one map for residue as a whole. Example if any residue of protein is
forming hydrogen bond with my ligand for certain time through bond A but
for the remaining time it forms through bond B, then I want the map to show
presence of hydrogen bond through one single line during the entire course
of simulation. Is it possible with gromacs?

Thanks in advance

More information about the gromacs.org_gmx-users mailing list