[gmx-users] ligand-water hydrogen bond

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 12 08:58:52 CEST 2004

On Tue, 2004-10-12 at 00:55, Yunfeng Hu wrote:
> 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.
Check the trjorder tool.
> Eric
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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