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.
HTH,
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 <n.gandhiau.gmail.com> 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
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Received on Wed Jun 03 2009 - 01:09:30 PDT
