Re: residue_rmsd.tcl via

From: Branko (
Date: Thu Aug 09 2012 - 08:38:14 CDT

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

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.
> Pozdravi,
> Michel
> ________________________________________
> 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
> Branko
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