VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 10 2009 - 16:25:00 CST

Hi,
  I'm assuming that the script you pasted from the tutorial ran your
computer out of memory somehow. How large was the trajectory you were
loading? I'm not sure from your description what happened in the second case.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Nov 04, 2009 at 08:48:29AM +0330, sarah k wrote:
> Hello dears,
> I'm an amateur in NAMD. I have problem calculating and plotting RMSD of a
> protein. I did any thing in the tutorial. I tried the script and pasted it
> from the tutorial in TK console. Suddenly all the windows of vmd got
> closed.
> As I understand, I should use the *.dcd file to calculate rmsd and then
> the output is a *.log file which can be used to plot the rmsd of my case.
> I used the available tools. Here are the results in "RMSD Trajectory
> Tool":
> I chose the *.dcd file downloaded from the VMD web. If I mark "top" for
> the ref, then click on RMSD in, a vmd window opens saying: Winvmd has
> encountered a problem and needs to close. When I close this window, it
> quits all vmd windows.
> When I open a *.pdb file, change the ref to average I see a new window:
> Rmsd vs frame "(protein) and name CA"
> a**a*NOTa** (as the plot I think!)
> In the main window of trajectory tool I see avg, sd, min and max as 0.
> When I try opening two files of the same protein (*.pdb and a**ws.pdb
> files), I face this error: vecdd: two vectors don't have the same size.
> A
> Would you please guide me? Thanks.
> Feel lucky forever,
> A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A
> Sarah Keshavarz
> A 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078