First of all, we have tested two +2->+1 mutation and we have the same
problem with both mutation.
Secondly, when doing a +2->+2 or +1->+1 mutation we got in the worst
case about 5kJ/mol difference, compared to experiment, while with the
+2->+1 mutation got a 30 kJ/mol difference compared to experiment.
/ Samuel
2010/1/28 case <case.biomaps.rutgers.edu>:
> 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".
>
> ...dac
>
>
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Received on Thu Jan 28 2010 - 06:00:03 PST
