From: Myunggi Yi (
Date: Mon Sep 11 2006 - 20:30:13 CDT

Dear users,

I'm aligning two structures with the following script.

vmd -dispdev text -eofexit << EOF > vmd-ali.out
mol load pdb ref-amt-in.pdb
mol load parm7 amt-in.parm7 rst7 amt-in.rst7

# align amt-in.rst7 to ref-amt-in.pdb to apply periodic box
set reference_sel [atomselect 0 "name CA and (resid 1 to 108)"]
set comparison_sel [atomselect 1 "name CA and (resid 1 to 108)"]
set transform_mat [measure fit $comparison_sel $reference_sel weight mass]

# molecule 0 is the same molecule used for $sel1
set move_sel [atomselect 1 "all"]
$move_sel move $transform_mat

measure rmsd $reference_sel $comparison_sel weight mass

$move_sel writecrdbox tra-amt-in.trj

The following is the end of the vmd-ali.out file

This file contains velocity info.
The Restartcrd has 30177 atoms.
This restartcrd file has box info.
Box Dimensions are 81.032997 76.070000 69.413002 90.000000
90.000000 90.000000
Info) Using plugin rst7 for coordinates from file amt-in.rst7
Info) Finished with coordinate file amt-in.rst7.
measure fit: no atom selection
invalid command name "move"
measure rmsd: no atom selection
invalid command name "writecrdbox"
Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
Info) Exiting normally.

What is wrong in my script?
I just copied the script from vmd website.

Best wishes,
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306
Office: (850) 645-1334