ok, thanks for your answer. If I just want to calculate for only one
tautomer its HOMO and LUMO orbitals, is it possible?
2010/11/23 case <case.biomaps.rutgers.edu>
> 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 Thu Dec 02 2010 - 02:00:03 PST
