use of 'measure hbonds'

From: DEEPESH AGARWAL (deepesh.iitd_at_gmail.com)
Date: Thu Jun 12 2008 - 23:54:34 CDT

Hi Monika,

Sorry, I did a typing mistake in writing commands in mail. But in
actual I did right selections, gave TCL commands in the same syntax
and wanted to find h-bonds between some of enzyme residues and water
molecules around it.

> set sel1 [atomselect top "protein and resid X"]
> set sel2 [atomselect top "water"]
>measure hbonds 5 150 $sel2 $sel1

 I got three lists in which first list is giving indices of hydrogen
atoms of water molecules too which should not be as it is meant to
consider non-hydrogen atoms, written in NAMD user's guide. Also third
list is giving indices of atoms other than hydrogen atoms too. Could u
throw some light over this unexpected outcomes and plz let me know the
correct elucidation of three lists. Thanks.
Have a nice day!

with regards,
Deepesh

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