VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Wed Oct 30 2002 - 10:54:13 CST

Hi,

Another thing that might help you with this in the current 1.8
pre-releases might be to use the new "measure hbonds" command. Type
"measure hbonds" at the VMD text console to get a summary of usage.
The function returns three lists of atoms, one for the donors, one for
the acceptors, and one for the hydrogen involved in the hbond. You
could probably cleverly combine some distance based atom selections
with the "measure hbonds" command to get a list of just the hydrogen
bonds you are interested in.

Justin

On Wed, Oct 30, 2002 at 10:37:02AM -0600, John Stone wrote:
>
> Hi,
> You can do distance-based atom selections in VMD using the
> "within" atom selection keyword. There are some examples of how to
> do this in the VMD user's guide here:
> http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node86.html#5239
>
> Let us know if you need more help.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Oct 29, 2002 at 09:22:48AM +0530, Y. U. Sasidhar wrote:
> > Hi,
> > I am using vmd ( 1.7.x ) on both windows and red hat linux 7.1 or higher to
> > visualize gromacs trajectories of peptides in water.
> > I want to detect simultaneous hydrogen bonding of i+4 NH and i CO with water
> > molecule. If I can display waters within 2.6 A of NH && CO I might be able
> > to do that. How do I do this in vmd.
> > regards,
> > Sasidhar
> >
> >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys