Re: [AMBER] small organic molecule

From: case <>
Date: Tue, 23 Nov 2010 13:34:41 -0500

On Tue, Nov 23, 2010, Rossella Noschese wrote:

> Dear Amber users, I usually work with peptides, but this time I was asked to
> make simulations of a small organic molecule. It's a
> 2,4-dichloro-5-nitrophenol.
> 1. Should I use antechamber to construct my molecule or can I simply draw it
> on xleap?

You definitely should consider using antechamber; the alternative is to start
from scratch and develop your own force field.

Antechamber requires as input a 3D structure with all hydrogens present. The
xleap interface could be useful in creating this.

> 2. It's demonstrated that this molecule is in equilibrium by proton exchange
> with other two structures and we want to know the preferred one and possibly
> the energy barriers between these three state. Which is the protocol I
> should follow to get these informations?

I don't understand what these "two other structures" are, but the general
questions asked in point 2 are way beyond what molecular mechanics can
answera. Studies of tautomeric equilibria generally require some combination
of quantum chemistry and solvation theory; studies of the kinetics of proton
exchange are more complex by another order of magnitude.

...good luck...dac

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Received on Tue Nov 23 2010 - 11:00:03 PST
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