AMBER Archive (2009)

Subject: Re: [AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy?

From: FyD (
Date: Sun Mar 22 2009 - 15:12:17 CDT

Dear Youn Kyeung Lee,

> The advanced tutorial1 says "Investigations showed that the dye has two
> minima that are in different conformations"(from SECTION1) before minimizing
> the conformations using Gaussian.

Just be aware there are several inaccuracies in this tutorial.

> I wonder what "investigations" should be done to identify conformations that
> have minimum energy.

Yes you are right, this is crucial to control the optimized geometry
of the minium/minima involved in charge derivation (used in the MEP
computation step). You might study E(QM)=f(considered_dihedral) or
compute g+/g- & t conformations for the considered dihedral(s). This
type of work might become time consuming, but in my opinion it is
important to do it before MEP computation. I see two main advantages
here: (i) you pick up the right/lowest conformation(s) for charge
derivation, and (ii) you get information about the potential energy
surface (PES) for the model involved in charge derivation: This last
point is important because these minimum/minima are those you should
observe during MD simulations... More you will get information about
your minimum/minima by QM (about its PES) for your model better you
will be able to understant MD simulation for the considered
biopolymer. Thus, you can check for wrong force field parameters for
the considered dihedral as well...

I tried to make it short ;-) but for sure this can be furthermore developed...

regards, Francois

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