AMBER Archive (2009)

Subject: Re: [AMBER] LYS-ASP

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Nov 27 2009 - 21:08:58 CST

On Fri, Nov 27, 2009, s. Bill wrote:

> I have one LYS residue close to ASP residue. According to QM
> calculation, it seems to be LYN and ASH, i.e. the proton prefers to be
> transefered to the carboxylate group rather than to stay on the amine
> group. So, which form the correct one for my simulation, LYS-ASP or
> LYN-ASH?

Might it be that the "QM calculation" was in vacuum, without waters around
(or without enough water around)? Such an environment would favor the neutral
species, but would not be very relevant to aqueous solution, which the ionic
species would be very much stabilized by hydration.

...dac

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