On Fri, Dec 21, 2007, Ilyas Yildirim wrote:
>
> I have analyzed some systems using icfe=2, and I have seen that it is
> better than icfe=1 when you have dummy atoms in initial/final states.
This is true, but the attractive thing about the softcore code is that there
is no longer a need for dummy atoms. If you want to mutate valine to
phenylalanine, you just set up the two endpoints in the "normal" way, and
proceed. No more figuring out what sort of dummy atoms should be where, or
making sure that you have all the parameters.
It could be that we should stick with icfe=2 for another release, but I think
most applications will be better off with the new code.
...dac
Received on Sun Dec 23 2007 - 06:07:38 PST
