On Thu, Jan 14, 2010, John E. Kerrigan wrote:
>
> One item to consider when setting up ambertools (amber11) with amber10
> as separate directories. When you use mm_pbsa, you will need to create
> a symbolic link in the amber11/src directory back to the mm_pbsa
> directory in the amber10/src directory. You will also need to create
> symbolic links to make_crd_hg between amber10/bin and amber11/bin as
> well as sander too.
Can you say why any of this is necessary? We set AmberTools 1.3 to unpack
into a new directory to avoid messing up what you might already have under
an amber10 directory. So mm_pbsa should continue to work as before, as far
as I can see. Am I missing something here? (e.g. do you not have an earlier
version of AmberTools installed, in the amber10 tree?)
[Among other things, what you describe sounds likely to break things when
Amber11 is eventually released, since that will completely populate the
"amber11" tree; symbolic links like you suggest back to amber10 would end up
with a nasty mixing of amber10 and amber11 trees....]
...dac
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Received on Thu Jan 14 2010 - 17:00:02 PST
