rmsd

From: divya nayar (divya.alchemist_at_gmail.com)
Date: Mon Nov 01 2010 - 03:30:11 CDT

Hi
I want to calculate RMSD of solvated peptide using Tcl script in VMD. I want
to find RMSD with respect to a reference structure i.e.minimized
crystallographic structure and not frame 0 of the trajectory (as mentioned
in rmsd.tcl given in tutorials). How can I use another molecule (minimized
crystallographic structure) in the same script to mention reference
structure appropriately in the 'atomselect' option?

Thanks,
Divya

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