VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Wed Jul 28 2010 - 07:59:08 CDT

OK, so I did answer your question already:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/16203.html

Leo

On Wed, Jul 28, 2010 at 2:55 PM, ban arn <ban.arn_at_gmail.com> wrote:
> Dear Leo
>
> Thanks.
>
> This is the command i'm using
>
> "rmsd_matrix -mol top -seltext name CA -frames all -fit none -o 2d_plot.txt"
> usage: rmsd_matrix ?-arg var?...
>   -mol <molid> (default: top)
>   -seltext <selection text> (default: backbone)
>   -frames <begin:end> or <begin:step:end> or all or now (default: all)
>   -fit <selection text> (default: backbone)
>   -o <filename>
> error: empty argument list or odd number of arguments -mol top -seltext name
> CA -frames all -fit none -o 2d_plot.txt
>
> Many Thanks
> Balaji
>
> On Wed, Jul 28, 2010 at 1:50 PM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>
> wrote:
>>
>> On Wed, Jul 28, 2010 at 2:45 PM, ban arn <ban.arn_at_gmail.com> wrote:
>> > Dear Leonard
>> >
>> > Thanks for the reply.
>> >
>> > I have saved trajectories containing only CA atoms.
>> >
>> > And in the command, i'm mentioning c-alpha atoms as "name CA in
>> > seltext",
>> > but it shows error as atomselect: cannot parse selection text: CA.
>> >
>> > Could you please tell me how to specify c-alpha atoms so that VMD can
>> > read
>> > it.
>>
>> Didn't I answer your question yesterday? What exactly is the command
>> that you are using (please copy and paste it)?
>>
>> Leo
>>
>> > Many Thanks
>> > Balaji
>> >
>> > On Wed, Jul 28, 2010 at 12:24 PM, Leonardo Trabuco
>> > <ltrabuco_at_ks.uiuc.edu>
>> > wrote:
>> >>
>> >> Dear Balaji,
>> >>
>> >> On Wed, Jul 28, 2010 at 12:50 PM, ban arn <ban.arn_at_gmail.com> wrote:
>> >> > Dear All
>> >> >
>> >> > I would like to plot 2D rmsd matrix for C-alpha atoms through my
>> >> > trajectories.
>> >> >
>> >> > Is any script available for this in VMD
>> >>
>> >> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/rmsd_matrix/
>> >>
>> >> Cheers,
>> >> Leo
>> >>
>> >> > Kindly advice.
>> >> >
>> >> > Many Thanks
>> >> > Balaji
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Leonardo Trabuco, Ph.D.
>> >> CellNetworks, BioQuant
>> >> University of Heidelberg, Germany
>> >
>> >
>>
>>
>>
>> --
>> Leonardo Trabuco, Ph.D.
>> CellNetworks, BioQuant
>> University of Heidelberg, Germany
>
> 

-- 
Leonardo Trabuco, Ph.D.
CellNetworks, BioQuant
University of Heidelberg, Germany