VMD-L Mailing List
From: divya nayar (divya.alchemist_at_gmail.com)
Date: Tue Nov 02 2010 - 11:53:26 CDT
- Next message: Eduard Schreiner: "Re: rmsd"
- Previous message: Axel Kohlmeyer: "Re: VMD text mode/unwrap"
- Next in thread: Eduard Schreiner: "Re: rmsd"
- Reply: Eduard Schreiner: "Re: rmsd"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
- Next message: Eduard Schreiner: "Re: rmsd"
- Previous message: Axel Kohlmeyer: "Re: VMD text mode/unwrap"
- Next in thread: Eduard Schreiner: "Re: rmsd"
- Reply: Eduard Schreiner: "Re: rmsd"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]