VMD-L Mailing List

From: syma khalid (syma_at_biop.ox.ac.uk)
Date: Fri Jan 28 2005 - 07:09:27 CST

You can loop over the trajectory using:

Set nf [molinfo top get numframes]
For {set i 1} {$i<$nf} {incr i} {

-Syma

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
Of bora erdemli
Sent: 28 January 2005 12:38
To: YOLANDA SMALL; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: measure hbonds

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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