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