VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Tue Sep 12 2006 - 02:03:30 CDT

There might be a problem with you selections. Try adding this to your
script after you define the selections:
puts [$reference_sel num]
puts [$comparison_sel num]
puts [$reference_sel get {resid resname}]
puts [$comparison_sel get {resid resname}]

good luck,

luis

Myunggi Yi wrote:
> 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
> quit
> EOF
> =====================================
>
> 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.
> 1
> atomselect0
> atomselect1
> measure fit: no atom selection
> atomselect2
> 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.
>
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node185.html
>
>
>
>