VMD-L Mailing List

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Sun Sep 19 2004 - 14:08:04 CDT

Alicia,

The structure you mentioned does not have any hydrogens (as usual in
crystallographic structures). Therefore, I think VMD is not able to
actually compute any hydrogen bond. You can add the corresponding
hydrogens by creating a psf file using psfgen (see the NAMD user's
guide or the NAMD tutorial at
http://www.ks.uiuc.edu/Training/Tutorials/)

Marcos

On Sep 19, 2004, at 8:42 AM, Alicia Hopkins wrote:

> On a windows box (using 1C3W.pdb as the protein model)
>
> I use the following commands:
>
> vmd> set reference_sel [atomselect 0 all]
> atomselect 0
> vmd> set cutoff 5
> 5
> vmd> set angle 45
> 45
> vmd> set hblist [measure hbonds $cutoff $angle $reference_sel]
> {} {} {}
>
> is my result. Previously, I was trying this on my Linux, and I was
> receiving the same result, any ideas?
>
> Cheers,
>
>
> Alicia C. Hopkins
> CIMAR / National High Magnetic Field Laboratory
> 1800 East Paul Dirac Drive
> Tallahassee, Florida 32310
> Phone: 850-644-1309
> Fax: 850-644-1366
> ahopkins_at_chem.fsu.edu