VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Sep 29 2011 - 12:46:25 CDT

The former. Be sure to heed the warning about overlapping selections.

On Sep 29, 2011, at 11:53 AM, Alex Hahn wrote:

> 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