VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Dec 30 2019 - 10:21:28 CST

Sorry, molecule 1 is not psf/pdb, rather /psf/restart.coor

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Mon, Dec 30, 2019 at 5:16 PM
Subject: RMSD pluging error
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>

Working on remote visualization with last vmd release, I have loaded
initial psf/pdb for a small molecule (molecule 0) in TIP3P and psf/pdb
after namd MD (molecule 1). I used various selections to get rmsd for the
small molecule

resname xxx
resid yyy
segname XXX
index 1 to 31

in all cases, backbone only, Top, align

error

measure fit: no atoms selected while executing "measure fit $sel1 $sel2". I
can't realize why no selection (I used successfully this plugin in the past
and don't remember whether there is a trick)
thanks for advice
francesco pieytra