residue_rmsd.tcl question

From: Christian Blouin (
Date: Fri Nov 02 2007 - 08:12:51 CDT



            We are attempting to apply the RMSD for individual residues
(NAMD tutorial) on a protein that has two residues with negative indexes.
The line:


            rmsd_residue_over_time top $sel_resid


            fails with the message:


            Calculating rmsd for frame 0

            Atomselect: cannot parse selection text: protein and resid -2
and noh


            Can anyone on this list help us understand the nature of this
problem and how to get around it.







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