[Chimera-users] hydrogen addition

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 28 09:31:47 PDT 2010

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.


"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.

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

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