AMBER Archive (2009)

Subject: Re: [AMBER] J coupling constant calculation

From: Gustavo Seabra (
Date: Tue Jun 02 2009 - 09:18:08 CDT

Hi Neha,

Amber doesn't provide such a script, but it is a very simple task to
write a little script that can do that using Karplus relations. All
you need is to use ptraj to generate the phi/psi angles, and use
Karplus relations to calculate the J-couplings.

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
Q: Why do mountain climbers rope themselves together?
A: To prevent the sensible ones from going home.

On Fri, May 29, 2009 at 1:24 AM, Neha Gandhi <> wrote:
> Hi List,
> I was wondering if there is a program/script to calculate theorectical
> Jcoupling from the AMBER or GROMACS simulations? How can we determine the
> conformational equlibrium (%) from the MD simulations?
> Help is appreciated.
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
> _______________________________________________
> AMBER mailing list

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