From: jeela keel (jeela22_at_gmail.com)
Date: Mon Jan 23 2012 - 12:45:22 CST

Hi

the script is the following
        setting the number of frames
         set sel1 [atomselect top "protein"]
        #set sel2 [atomselect top "resname SOL "]
        set sel2 [atomselect top "resname SOL and pbwithin 4.00 of protein
"]

        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"

thank you jeela

On Mon, Jan 23, 2012 at 12:55 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Mon, Jan 23, 2012 at 12:35 PM, jeela keel <jeela22_at_gmail.com> wrote:
> > Hi All,
> >
> > I used a different dcd file that has less frames (only 263). This time it
> > gave same error but in the frame 262 before the last one.
> > is it possible that my sections are causing the problem since the
> measure
> > command is using the selections? I am selecting the protein and the
> > water surrounding the protein.
> >
> > ERROR) measure gofr: bad frame range given. max. allowed frame#: 262
>
> a-ha! yes. if you have 263 frames, the last frame is frame number 262.
> the frame numbers start from 0. if you want to use an explicit number of
> frames, then you have to subtract 1 from the total number of frames to
> get the last frame number.
>
> axel.
>
>
> >
> > Thank you
> >
> > Jeela
> >
> >
> >
> > On Mon, Jan 23, 2012 at 12:18 PM, jeela keel <jeela22_at_gmail.com> wrote:
> >>
> >> yes I am doing similar way to get the number of frames.
> >>
> >> jeela
> >>
> >>
> >> On Mon, Jan 23, 2012 at 11:01 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >>>
> >>>
> >>> Are you correctly querying the number of frames with something like:
> >>> set number_frame [molinfo top get numframes]
> >>>
> >>> Cheers,
> >>> John Stone
> >>> vmd_at_ks.uiuc.edu
> >>>
> >>> On Mon, Jan 23, 2012 at 10:56:43AM -0500, jeela keel wrote:
> >>> > On Mon, Jan 23, 2012 at 10:29 AM, Axel Kohlmeyer
> >>> > <akohlmey_at_gmail.com>
> >>> > wrote:
> >>> >
> >>> > isn't the error message is self-explanatory?
> >>> > your argument to the "last" flag is obviously incorrect.
> >>> >
> >>> > axel.
> >>> > >
> >>> > Hi Axel
> >>> >
> >>> > set gr1 [measure gofr $sel1 $sel2 delta .1 rmax 10.0 usepbc
> >>> > 1 selupdate 1 first 1 last $number_frame step 1]
> >>> >
> >>> > Thank you for your suggestion, I am using the last number for
> the
> >>> > frames which is 1000 frames but it stops in frame 500 and give
> me
> >>> > the
> >>> > error
> >>> > jeela
> >>> >
> >>> > --
> >>> > Dr. Axel Kohlmeyer
> >>> > akohlmey_at_gmail.com http://goo.gl/1wk0
> >>> >
> >>> > College of Science and Technology
> >>> > Temple University, Philadelphia PA, USA.
> >>>
> >>> --
> >>> NIH Resource for Macromolecular Modeling and Bioinformatics
> >>> Beckman Institute for Advanced Science and Technology
> >>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> >>> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
> >>
> >>
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>