AW: residue_rmsd.tcl via

From: Norman Geist (
Date: Thu Aug 09 2012 - 09:44:28 CDT



A tcl script is plain text, so just look to the script to see what it does.
What I could imagine is that you try to start VMD with the script as input,
but this is likely not the way the script works. I guess you have to load
your molecular system and then source the script from the VMD console.


Norman Geist.


Von: [] Im Auftrag
von Branko
Gesendet: Donnerstag, 9. August 2012 15:38
An: Michel Espinoza-Fonseca; namd-l
Betreff: Re: namd-l: residue_rmsd.tcl via


Hvala Michel.

Matter of fact there is no any output. There is no dat file or any other
output. I try to put all files in the directory which are placed in the same
'disc' (as defined by windows) to overcome long paths from file to file,
also to put all files in VMD installation directory (not recomendedm,
but..), and nothing. Also downloaded the last version of the script from the
NAMD tutorial files, and inspect the text, this is general scrpt and should
be easily applied to any trajectory. I think to try to load files (psf and
dcd) from console, and then to try to invoke script.

Kind regards


On 8/9/2012 3:18 PM, Michel Espinoza-Fonseca wrote:

Dear Branko,
Could you please be a bit more specific on what exactly is the problem
you're encountering? I'm pretty sure that "something" is actually happening,
i.e., most likely a .dat file containing RMSD per residue is written in your
working directory.
From: [] On Behalf Of
Branko []
Sent: Thursday, August 09, 2012 7:50 AM
To: namd-l
Subject: namd-l: residue_rmsd.tcl via
Dear NAMD users,
Is anybody succeed to execute script 'residue_rmsd.tcl' in Windows VMD
(1.8.7) on their own protein. Likely, main question is where: fie.psf,
file.dcd and residue_rmsd.tcl script should be placed. I try to put
all files in one directory, but after loading psf file in VMD and
loadinfg DCD 'into' psf, then invoking 'source residue_rmsd.tcl' in
console nothing happen. Think that this question is more suitable for
namd-l than vmd-l because queering namd tutorial files.
Thank you for any advice

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