[gmx-users] ligand-water hydrogen bond

[Yunfeng Hu]

Hi, I am trying to analyze the number of hydrogen bonds between small 
ligand and surrounding water/enzyme from a md simulation. However there 
are ~10,000 water molecules and  g_hbond ran out of memory. As a matter 
of fact, I am only interested in the water near the ligand. Is there a 
way that I can define a group (including protein and water) centered 
within 5 angstrom of the ligand? I have yet figured out how to use 
make_ndx to do this. Thanks.

Eric