[gmx-users] ligand-water hydrogen bond

Yunfeng Hu yunfeng at scripps.edu
Tue Oct 12 00:55:14 CEST 2004

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.


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