VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jun 19 2008 - 09:31:53 CDT

On Thu, 19 Jun 2008, Y. U. Sasidhar wrote:

S> When I display a helix from a PDB file and choose H-bonds representation no
S> hydrogen bonds are displayed. This is due to lack of donor hydrogens in
S> crystal structures.
S>
S> How can we display hydrogen bonds based on **only** donor- acceptor distance?

one major point about the definition of hydrogen bonds is, that
the distance between donor and acceptor alone is _not_ a sufficient
criterion. so if you don't have the hydrogens, you cannot tell where
the hydrogen bonds are. you can only tell where they will for sure
not be.

S> I searched user guide and vmd site; but could not come across an answer.

of course not. you first will have to place hydrogens at likely
places, e.g. by molecular modeling.

now, to visualize distances between atoms that fall below a
certain threshold distance, you can use the dynamic bonds feature...

cheers,
   axel.

S>
S> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.