From: John Stone (
Date: Fri Apr 10 2015 - 01:55:52 CDT

  If I understand you correctly, it seems that you're using a Tcl script
from one of the tutorials? Normally you would run the Tcl script inside
of VMD, e.g. by running a command such as:
  source script.tcl

I don't know which specific script you're using nor what it says so
I can't comment on your other questions related to "workdir" etc.
If you provide the URL where you got the script from that might be

  John Stone

On Sat, Mar 21, 2015 at 03:06:42PM -0700, Akshata Rudrapatna wrote:
> Hello:
> I am currently trying to merge sixty copies of the cowpea mosaic virus
> capsid molecule into one large solvated molecule (like the one provided
> for the satellite tobacco mosaic virus tutorial). I found the
> MergeMultiFramesPDB Tcl file, but I had a few questions regarding it.
> 1) Do I need to download Tcl itself separately from NAMD and then
> implement this code?
> 2) Where do I program the code? Do I just use the TkConsole?
> 3) Where in the code do I need to provide file paths? Is "workdir" a part
> of the code or a reference to providing the file path to the work
> directory?
> I have already tried to use the TkConsole to utilize the code but it has
> not worked and does not yield any new files.
> Any help is greatly appreciated.
> Thanks,
> Akshata Rudrapatna

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349