From: sarah k (
Date: Tue Nov 03 2009 - 23:18:29 CST

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"
●▬● (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 –ws.pdb files),
I face this error: vecdd: two vectors don't have the same size.

Would you please guide me? Thanks.
Feel lucky forever,
                                      Sarah Keshavarz