[Chimera-users] hydrogen addition

[Elaine Meng]

Hi Forbes,
AddH is not minimizing an energy function.  It does attempt to avoid clashes, and by default ("also consider H-bonds") also to add the hydrogens of hydroxyls at positions that enable hydrogen-bonding, but the process is neither combinatorial nor an optimization.

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html>

"Although hydrogens are placed to avoid clashes and form hydrogen bonds where possible, they are not energy-minimized, and a globally optimal network in terms of the number of H-bonds or total H-bonding energy is not necessarily found."

The hydrogens are added using the bond lengths from the Amber force field (parm99 prameter set), shown in a table in the help page (URL above).

For a more intensive approach to adding hydrogens, you could try the Reduce program from the Richardson Laboratory.  A more detailed description and some links are provided in the bottom section of the AddH help page.

Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 28, 2010, at 7:13 AM, Forbes J. Burkowski wrote:

> Hi:
> We are trying to assess relative strength of hydrogen bonds using a
> formula such as that on page 1336 of the paper by Dahiyat et al. (Protein
> Science, 1997 (6) 1333-1337).  This formula takes angle information into
> account, but it requires the position of the hydrogen atom.  My question
> is: If I use AddH, do I get a position of the H atom that is reliable
> enough to allow us to use this formula?
> 
> It occurs to me that AddH might be computing a position that would
> minimize the value of the energy function specified on page 1336, but I am
> not sure if this is the case.
> 
> Can you give us any advice on these issues?  Is there another formulation
> that I could use with Chimera?
> 
> Best regards,
> Forbes Burkowski
>