Re: AMBER: nanotube parameters

From: David A. Case <>
Date: Fri, 17 Dec 2004 15:34:31 -0800

On Fri, Dec 17, 2004, MURAT CETINKAYA wrote:
> I am trying to establish some parameters for a single walled carbon
> nanotube.
> Leap wants an angle parameter for C-C-C bonds, so I used parmcal and got
> 65.690 and 120.000 as results. However, in the literature I found some
> values like 562 kJ/mol (=134 kCal/mol).

You should not necessarily assume that "C" is a good representative of a
carbon nanotube. Also be aware that Amber uses an energy function for angles
like this:

    E = K * (delta-theta)**2

where delta-theta is measured in radians, and there is no factor of (1/2)
in the equation. Keep these in mind as you compare parameters, since the
literature functions may be different.

I doubt that any atoms one usually sees in biomolecules really looks much like
what one has in a nano-tube.

....good luck....dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Dec 17 2004 - 23:53:00 PST
Custom Search