From: Vermaas, Joshua (
Date: Mon Oct 09 2017 - 10:09:04 CDT

I think your problem is running things with tclsh. atomselect is not a typical Tcl command. VMD adds that to the language. So typically you'd run a script by sourcing it from within VMD ("source script.tcl") or by passing it in as a command line argument (vmd -e script.tcl).


On 10/09/2017 12:20 AM, Seera Suryanarayana wrote:
Dear vmd users,

I have 15 PDBs and I have to calculate the RMSD for all the 14PDBs with first PDB.
I have executed one tcl script with tclsh command. The script has the following information...

set sel1 [atomselect 0 "backbone"]
set sel2 [atomselect 1 "backbone"]
measure rmsd $sel1 $sel2

As example I ran the script with 2 PDBs and I got following error.

Invalid command name "atomselect"

    while executing

"atomselect 0 "backbone""

invoked from within

"set sel1 [atomselect 0 "backbone"]"

(file "rmsd.tcl" line 1)

Kindly tell me whats wrong in the script.

Thanks in advance

Graduate student