VMD-L Mailing List

From: jeela keel (jeela22_at_gmail.com)
Date: Mon Jan 23 2012 - 15:06:10 CST

On Mon, Jan 23, 2012 at 3:13 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Mon, Jan 23, 2012 at 1:55 PM, jeela keel <jeela22_at_gmail.com> wrote:
> > Hi Axel,
> >
> > added the missing things, it should be complete now. let me know what you
> > think?
>
> this script still has obvious errors (outside of your gofr issue).
>
> why can't you just attach the entire script that you have?
> what is the big secret that you are hiding? you are just
> wasting your time and won't get proper help.
>
> the script is based on the following
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-8012/gofr-script.tcl

> on top of that, you obviously didn't pay attention to what
> i wrote before about the frame numbers being 0-based
> and not 1-based. if you want all frames, why don't you
> just use -1 as the "automatic" last frame number?
>

yes if you have payed attention to my previous email I have tried the -1
 last frame and it gave same error

>
> also, is there any reason that you are not using the
> gofr gui plugin? as far as i can tell, there is nothing
> in your script that the plugin does not do. why reinvent
> a wheel, particularly one that doesn't go round?
>

thanks for your help, I will take a look at the gofr plugin

jeela

> > set outfile [open gdr.dat w]
> > set $number_frame [molinfo top get numframes]
>
>
>
> > set sel1 [atomselect top "resname X"]
> >
> > #set sel2 [atomselect top "resname SOL "]
> > set sel2 [atomselect top "resname SOL and pbwithin 4.00 of
> resname X
> > "]
> >
> > set gr1 [measure gofr $sel1 $sel2 delta .1 rmax 10.0 usepbc 1
> > selupdate 1 first 1 last $number_frame step 1]
> > set r [lindex $gr1 0]
> > set gr2 [lindex $gr1 1]
> > set igr [lindex $gr1 2]
> > set i 0
> > foreach j $r k $gr2 l $igr {
> > puts $outfile1 "$j $k $l"
> > close $outfile
> >
> > jeela
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>