From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Thu Jun 19 2008 - 09:46:51 CDT

Hi Sasidhar -

You can place the hydrogens by building a PSF file and new PDB file
(see the VMD tutorial on how to do this with psfgen) and running a
short equilibration run (see NAMD tutorial) to relax (equilibrate) the
protein. This last step is necessary since the positions of hydrogens
psfgen uses are an approximation, and ideally you would want to
analyze the protein in an energetically favorable conformation. Then
you can display hydrogen bonds based only on acceptor-donor distance
by writing a script which selects the relevant atoms and draws a line
between them if they are within your distance cutoff. Alternatively,
you could just do this in VMD with the equilibrated protein, but with
a very large cutoff angle, which would essentially be the same as
giving a larger weight to your distance cutoff.

Tutorial website: http://www.ks.uiuc.edu/Training/Tutorials/

-Eric

On Jun 19, 2008, at 7:34 AM, Y. U. Sasidhar wrote:

> When I display a helix from a PDB file and choose H-bonds
> representation no hydrogen bonds are displayed. This is due to lack
> of donor hydrogens in crystal structures.
>
> How can we display hydrogen bonds based on **only** donor- acceptor
> distance?
>
> I searched user guide and vmd site; but could not come across an
> answer.
>
> --
> with best regards,
>
> Sasidhar
>
>
>

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu