VMD-L Mailing List

From: Alex Hahn (alexander.hahn_at_richmond.edu)
Date: Thu Sep 29 2011 - 11:53:13 CDT

Hi all,

In the Hydrogen Bonds plug-in for VMD... let's say I put "resid 1" for
Selection 1 and "resid 2" for Selection 2. Would it show me when resid 1 and
resid 2 hydrogen bond ONLY? Or does it show ANY time both residues hydrogen
bonds with ANYTHING (i. e. itself, with solvent molecules, etc.)?

The same question goes for multiple residues. So if I put "resid 1 to 137"
for Selection 1 and "resid 140 to 282" for Selection 2, would it show me
whenever these two chains hydrogen bond with EACHOTHER only? Or does it show
me any hydrogen bonds these two chains make with ANYTHING (i. e. itself,
with solvent molecules, etc.). I'm trying to analyze the number of
interdomain h-bonds in a trajectory.

Thanks,
Alex