VMD-L Mailing List

From: bora erdemli (boraerdemli_at_yahoo.com)
Date: Fri Jan 28 2005 - 06:38:12 CST

Hi All;

there is a tcl command 'measure hbonds'command the
usage is as follows:
 
measure hbonds 3.5 30 $sel1 $sel2
3.5 is the cut off distance and 30 is the cut off
angle.
$sel1 is the donor of the hydrogen bonds
$sel2 is the acceptor of the hydrogen bonds

if you put this command line in a for loop which is
over the trajectory and calculate the number of
hydrogen bonds for each frame by using some TCL
scripting. you may make a plot of time versus Hbond
graph. If you do not do it I may write a simple
instructive code for you.

sincerelu yours

--- YOLANDA SMALL <yas102_at_psu.edu> wrote:

> Hello,
>
> I have a series of pdb files which I obtained by
> converting a trajectory file to
> pdb frames.
> Is there a VMD script somewhere that measures the
> hbonds between certain atoms
> in each frame and outputs the frequency of hbonds as
> a function of time?
>
> Thanks,
> Y Small
>

=====
Sabri Bora Erdemli
Koc University
Computational Science and Engineering
Research and Teaching Asistant
Koc Universitesi pk.218 34550
sariyer Istanbul/TURKEY
tel no: 02123381736
          05326512523
 
 

                
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