VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Fri Apr 01 2005 - 13:42:48 CST

Hi,

I cannot really help you with the atom selection, that depends on your
system and what you want to do. If the problem you are having is that
you don't know how to select atoms in VMD then you could take a quick
look at the VMD manual.

Best,

Luis

Wen Li said the following on 04/01/05 14:23:

>Dear Dr. Gracia,
>
>Thanks you very for your kind help.
>
>I followed the procedure that you wrote. Now I am wondering what should I
>fill in the "selection box" - this is an RNA molecule, and I want to
>align all P atoms to the reference.
>
>Thanks,
>Wen
>
>On Fri, 1 Apr 2005, Luis Gracia wrote:
>
>
>
>>Hi,
>>
>>the rmsdtt plugin works the same way as the 'rmsd tool' plugin, except
>>it loops through trajectories. For that reason a few options were added,
>>plus some improvements over the 'rmsd tool' plugin. This new options are
>>explained in the web;
>>http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/index.html
>>
>>For your case you can:
>>- load the reference structure in another molecule and select it as the
>>'top' molecule.
>>- press the 'only active' button to update the list in the rmsdtt
>>plugin. The list should now include all the molecules (or trajectories)
>>you want to calculate the rmsd, included the reference.
>>- select the 'top' option in rmsdtt.
>>- activate the 'trajectory option' in rmsdtt.
>>- choose your 'plot' and 'save' options.
>>- press the rmsd button to get an rmsd (optional)
>>- press the align button to align.
>>- press the rmsd button again to obtain the final rmsd.
>>
>>Hope this helps.
>>
>>Luis
>>
>>Wen Li said the following on 04/01/05 12:15:
>>
>>
>>
>>>Hello Everyone,
>>>
>>>I am wondering if there is a User's guide for RMSDTT in vmd - I am trying
>>>to align an MD trajectory to a reference structure which is not in the
>>>trajectory.
>>>
>>>
>>>
>>>From the window of RMSD trajectory Tool, it seems to me like that the
>>
>>
>>>reference structure comes from a frame of the trajectory. If my reference
>>>is not in the trajectory, how I can make it? My trajectory file was
>>>generated from AMBER.
>>>
>>>I appreciate any help.
>>>
>>>Wen
>>>
>>>
>>>
>>> 

-- 
Luis Gracia, PhD
Department of Physiology & Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Box 75
New York, NY 10021
Tel: (212) 746-6375
Fax: (212) 746-8690
lug2002_at_med.cornell.edu