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?
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?
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Received on Tue Nov 23 2010 - 08:00:03 PST
