From: Dong Luo (us917_at_yahoo.com)
Date: Fri Nov 04 2011 - 14:42:09 CDT

Why will you expect it to be summed to 100%? H-bond is not guaranteed to exist at any time. If there is no H-bond at all, you always find nothing in the results. Dong ________________________________ From: lina <lina.lastname_at_gmail.com> To: vmd-l_at_ks.uiuc.edu Sent: Thursday, November 3, 2011 10:06 AM Subject: vmd-l: How to understand the occupancy? Hi, When I used analysis -hydrogen bonds, it showed me the occupancy is 1.96%, several ones shared the same value. I added all those percentage, it won't reach 100%. and suppose there is 51 frames. Found 15 hbonds. donor             acceptor         occupancy Seg{}-MET77-Main     Seg{}-AAA85-Side     1.96% Thanks for any suggestions, Best regards,