VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Wed Jul 28 2010 - 07:50:53 CDT

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