VMD-L Mailing List

From: divya nayar (divya.alchemist_at_gmail.com)
Date: Tue Nov 02 2010 - 11:53:26 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?

Also, when a selection of "backbone" of peptide is made in atomeselect, does
it include havy atoms from the side chains as well?

Thanks,
Divya Nayar