Re: [AMBER] TI with soft core potentials

From: case <>
Date: Thu, 28 Jan 2010 08:10:06 -0500

On Thu, Jan 28, 2010, Samuel Genheden wrote:

> >> We have tried to mutate a +2 ligand to +1 ligand and got much worse
> >> results, compared to when we mutated a +2 to +2 ligand.

I agree that there is no general reason to distrust the results, simply
because you are changing the net charge. But energies are more sensitive
when you make big changes (like changing the overall charge), so you may be
seeing limitations of the force field. Beyond that, the sampling problem is
often worse, since changing net charge can have long-range conformational
effects that you are not seeing. Finally, be wary of drawing general
conclusions from a small number (1?) of examples.

Beyond that, without knowing what "much worse results" really means, it's hard
to say more. Of course, you should always check your results carefully, and
not just when the results look "bad".


AMBER mailing list
Received on Thu Jan 28 2010 - 05:30:02 PST
Custom Search