VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Mon Jul 23 2007 - 10:32:46 CDT

On Mon, Jul 23, 2007 at 10:28:01AM -0500, Leonardo Trabuco wrote:
> Dear Hori:
>
> On Mon, Jul 23, 2007 at 04:50:10AM -0700, hori koshii wrote:
> > Just wonder if there is any option for saltbr package that may allow the printout of total number of saltbridges throughout the trajectory (#saltbr vs. frame). I tried but the log file only prints out the "total" numbers for the whole trajectory, instead of numbers in each frame. I just wonder if there is any extra options beside the one found on this page (http://www.ks.uiuc.edu/Research/vmd/plugins/saltbr/)
> > or can anyone suggest a easy way to do so?
>
> There is no such extra option. Assuming you don't wanna change the code,
> one way to do it is to write a small script that loops over all frames
> and runs saltbr on each of them (option -frames now). You would generate
> a log file for each frame and then get the number of salt bridges from
> each config file with grep or something like that.
>
> So your script would look like (not tested):
>
> set nframes [molinfo top get numframes]

Sorry, this should be numframes instead of nframes...

[...]

Cheers,
Leo 

-- 
Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign