From: Vermaas, Joshua (
Date: Wed Sep 13 2017 - 13:41:30 CDT

Hi Thomas,

There are a couple of different ways of going about it. If you have a psf loaded, you will find that in general polar hydrogens tend to have above-average charges. So something like "hydrogen and charge > 0.2" is the first way I learned to do this. Working with bonds, you can also pick things out based on what they are bonded to: "hydrogen and withinbonds 1 of name \"O.*\" \"N.*\" \"S.*\"", where the "\" character is used only in scripts so that tcl doesn't end your string early (they aren't needed in the graphical representations window).


On 09/13/2017 12:04 PM, Albers, Thomas wrote:


Is there any keyword in VMD that selects polar hydrogens (i.e. those bound to N, O and possibly S)?