Re: how to use measure hbonds to calculate occupancy of all hbonds in simulation?

From: Dong Luo (us917_at_yahoo.com)
Date: Tue May 15 2007 - 18:27:01 CDT

With the interest of learning more about tcl, I write
a script to accomplish the things you want. It
requires the same arguments as measure hbonds and you
may redirect the results to a file by adding a file
name as an extra argument otherwise it is send to the
display. In response to your second question, I guess
what you need is running the script twice with the two
selection you mentioned switched.

--- lnubiofox <lnubiofox_at_163.com> wrote:

> 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

 
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