Hi Alex, I would not worry, just use the "also consider H-bonds" method when adding hydrogens in Chimera. That method is the default. In fact hydrogens might be totally irrelevant to DelPhi depending on what DelPhi parameter files you are using. If I recall correctly, their "default.crg" and "default.siz" files are for use on structures without hydrogens. By far the most difficult thing is making sure parameters are assigned correctly and that the net charge of your protein in the delphi log file is what you expect. Sometimes people use parameter files with hydrogen names that don't match those in the structure and the net charge of the protein is reported in the log file as a huge negative non-integer. 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 http://www.cgl.ucsf.edu/home/meng/index.html On Aug 4, 2009, at 10:21 AM, Alex Gawronski wrote:
Thanks for the info!
I was just worried that the added hydrogen atoms would not be in the minimal position. They do move a little from the minimization. Do you think that is significant?
Alex Gawronski