Re: AMBER: help me for filling a nanotube with water??

From: Thomas Steinbrecher <>
Date: Wed, 13 Aug 2008 09:40:22 -0700 (PDT)

Hi Jaber,

leap is able to fill cavities in your molecule as well as pack a solvent
buffer around them. If you just try

solvatebox <nanotube> TIP3PBOX 12

in leap, you will see the interior filled with water molecules as well as
a water box around the tube. Even if leap puts to many or to few waters in
there, the number should equilibrate pretty quickly if the tube is

My first guess is that the Amber force field should not be particularly
good or bad for a nanotube (you might have to build a frcmod file that
specifically describes bonding in a nanotube, though) since it is a
structure that shouldn't do much in an MD simulation anyway. The critical
question might be what kind of question about nanotubes do you plan to
adress by doing an MD simulation of it?

Kind Regards,


Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Wed, 13 Aug 2008, Markus Kaukonen wrote:

> Dear Dr Jaber Jahanbin Sardroodi,
> I'm not sure at all how well Amber MM force field is suitable for nanotubes.
> What I know is that nanotubes have been simulated with the
> density-functional based tight-binding method
> which is in amber (it is called QM in this context). So maybe you
> could try using Amber-QM for nanotubes.
> I'm also starting to look at this business, so all comments are welcome.
> Probably if you do not have any organic molecules in your system, some
> other molecular mechanics program than AMBER might be computationally
> much more efficient, with a force field tailored for carbon.
> Terveisin, Markus
> On Tue, Aug 5, 2008 at 4:39 AM, Jaber Jahanbin Sardroodi
> <> wrote:
>> Dear Amber professional,
>> I need to fill a carbon nanotube with water molecules (using leap),
>> unfortunately I do not know what I do. Can anyone help me?
>> Sincerely,
>> Dr Jaber Jahanbin Sardroodi
>> Department of Chemistry, Faculty of Basic Sciences, Azarbaijan
>> University of Tarbiat Moallem, Tabriz, Iran
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Received on Sun Aug 17 2008 - 06:07:12 PDT
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