From: niaz poorgholami (
Date: Fri Nov 11 2011 - 13:21:24 CST

Hi John
 thank you for your help.It sounds that I should first merge the nanotube
and polymers pdb files
and then place the polymers in a appropriate position respect to CNT
surface and then
using VMD main/File/save coordinate save the structure created. Is that all
I need
to do?
and another question,having a pdb file for CNT and the other one for
polymer, can I merge CNT and polymer
or perhaps I need something else?
              thank you

On Fri, Nov 11, 2011 at 10:21 PM, John Stone <> wrote:

> Hi,
> 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.
> Cheers,
> 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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