From: LEWYN LI (ll2150_at_columbia.edu)
Date: Tue Sep 06 2005 - 11:12:35 CDT
Sergio,
There is a script at the NAMD website called "rmsd.tcl" at:
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node10.html
Alternatively, you could try the "rmsd" function in VMD. It is
under "Extensions" -> "rmsd" in the VMD Main Window.
You need to load both structures into VMD, select one as the
reference and then align the two structures. Then you can compute the
rmsd for each amino acid.
Finally, if you would like to compute the rmsd of the CA's of two
amino acids in two structures, it might be quicker to just compute the
value by hand.
Hope this helps!
LEWYN
On Tue, 6 Sep 2005, Sergio Anis wrote:
>
> hi everybody:
>
> does anyone have a script to calculate the rmsd of CA for two amino
> acids (one is the right structure and the other is an attempt to guess
> its coarse configuration), or something similar I can modify?
>
> I really appreciate it if you can share it with me.
>
> best regards to all
>
> Sergio
>
>
>
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