VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 23 2012 - 12:51:41 CST

On Mon, Jan 23, 2012 at 1:45 PM, jeela keel <jeela22_at_gmail.com> wrote:
> 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"
>

this is not a complete script and doesn't work.

axel.

> 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.
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.