VMD-L Mailing List

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Tue Aug 25 2009 - 22:50:43 CDT

Although there is a selection macro "polar", it applies only to
residue names.

If you have a psf/pdb loaded, you could select polar hydrogen atoms
by charge (say larger then +0.15) like

name ".*H.*" and charge >=0.15

Alternatively, you could select by atom type.
You'll have to know the atom types, though. The types will vary
depending on the force field you are using. If you do not use a force
filed,
i.e. you also do not have a psf file, you'll most probably will have
to select like
name ".*H.*" and within 1.5 of name ".*O.*" ".*N.*" ".*S.*"
(I'm using wild cards because I don't know what the real atom names
are.)
The above selection will not catch hydrogen atoms at aromatic groups,
though,
which can also have a charge of >0.1, but those usually do not
participate in H-bonds.

eddi

On Aug 25, 2009, at 10:13 PM, poker_at_physics.usyd.edu.au wrote:

> I've been wondering - is there a way to select just the polar
> hydrogens in VMD?
>
> This is what I'm after - I'm inspecting a semi-buried portion of a
> protein with
> a h-bonding network, and wish to visualise what the sidechains are
> doing.
> However, I've got an all-atom model where the aliphatic/aromatic
> hydrogens are
> cluttering up the display, and I haven't found an easy solution to
> choose only
> the polar hydrogens that can h-bond.
>
> I guess this is a feature request for a selection keyword that
> includes only
> polar hydrogens?
>
> thanks,
> P.

=====================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================