From: lnubiofox (
Date: Tue May 15 2007 - 09:21:33 CDT

Dear users,
      I submitted a mail named "how to calculate the hbonds occupancy" to mailing list the day before yesterday.Thank Axel Kohlmeyer,Gianluca Interlandi,Jojart Balazs and Richard Wood for the rapid replies which inspirit me a lot. I learned the usage of command "measure hbonds" and checked the information related to this command in the mailing list. However,I still have some questions. 1. I want to extract the occupancy of all the H-bonds existed during the simulation time,like "Glu50-Ser62 77.2%" which means there is a hydrogen bond between donor residue Glu50 and acceptor Ser62,the percentage of frames formed this hydrogen bonds is 77.2%. In the mailing list I learned maybe put the "measure hbonds" command in a for loop over the trajectory will calculate ONLY ONE given hbonds' occupancy each time,then how to measure how many hbonds exist during simulation and calculate the percentage of frames it exist in for all of them? 2. there is a warning:"When using 'measure hbonds', you should avoid having the same atom listed in both the $selection1 and $selection2 parameters if you desire to have reliable results",then how to caculate all hbonds between two parts of the protein? For example, resid 1 to 49 and resid 50 to 108 ? 3. the output of the command is like this{191 473},how to transform it into the residue-residue form mentioned above automaticly in the tcl script ? And is there any other ways to solve this problem such as other free sofewares or an existed script? Any suggestions will be highly appriciate.Thanks in advance and looking forward to your reply. ^_^ Best regards, Yuan Liu Liaoning university P.R.China