Re: AMBER: how to excite a single residue ?

From: Pradipta Bandyopadhyay <>
Date: Thu, 10 Mar 2005 10:54:34 +0530 (IST)

If you are talking about electronic excitation then at least for the TRP
residue you have to use a quantum mechanical method applicable to excited
state (even if you talk about vertical transition as opposed to an
adiabatic one, the charge distribution can be very different in an
electronically excited state). AMBER force field as such is not meant for
electronically excited state. AMBER8 has some QM/MM methods - I don't know
what it has - if one of these can be used for excited state you can start
from there. Other wise you need a code which can do QM/MM dynamics, where
the QM method can be used for excited state.

Koji Ando has papers in a similar subject. Of course Mike Zerner's papers
would be useful too.

> Hi,
> I want to follow the femtosecond dynamics of macromolecular hydration by
> MD simulation. Experimentally, a femtosecond excitation is given to the
> solute which creates a dipole. This dipole gives rise to an
> instantaneous electric field on the solvent molecules. The interaction
> of solvent permanent dipoles with the electric field is studied to get
> the solvation time correlation function. This has been studied
> experimentally on proteins which has a TRP residue on its surface. This
> residue is excited with a femtosecond excitation in the experiment.
> Now, if I want to follow this with MD simulation, how do I excite or
> perturb the TRP residue ? Has anybody done this kind of studies ? Please
> help.
> Regards,
> -Priti
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

Dr. Pradipta Bandyopadhyay
Assistant Professor
Dept. of Biotechnology
Indian Institute of Technology, Guwahati
Phone: 91-361-258-2213 (office)

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Mar 10 2005 - 05:53:00 PST
Custom Search