From: John Stone (
Date: Fri Nov 11 2011 - 12:51:11 CST

  This sounds to me like something you would want to do using some
scripting with atom selection "move" operations if you already have
the polymers merged into the same VMD "molecule" as the nanotube.
If so, once you update the positions with the script(s), you could
then write the final structure out to a file using the "write"
atom selection subcommand, or by using the VMD graphical interfaces.

Perhaps someone else can give you more specific guidance or suggest
an existing tool for this purpose.

  John Stone

On Fri, Nov 11, 2011 at 10:01:47PM +0330, niaz poorgholami wrote:
> Dear all
> I have a pdb file for carbon nanotube and a pdb file for polymers and I
> want to place polymer molecules on a surface of CNT. I can move polymers
> by VMD main/mouse/move but I want to locate polmers in a appropriate
> position with respect to
> CNT surface and then save the created structure. would you please help me
> how to place polymers and then save
> that ?
> niaz

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