VMD-L Mailing List

From: poker_at_physics.usyd.edu.au
Date: Wed Aug 26 2009 - 02:05:44 CDT

Ok, is working since I've been using charmm ffs. Thanks,
P.

Quoting Schreiner Eduard <eschrein_at_ks.uiuc.edu>:

> 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/
> =============================================
>
>