On Thu, Sep 22, 2011, truongco nguyen wrote:
>
> I am trying reinstall Amber11 with AmberTool 1.5.
This is not a very helpful summary, since we don't know what the "old"
installation consisted of, and what the "new" one has.
>
> Everything seem good until one of user use the nmode to calculate entropy.
Three notes: (a) nmode is not a part of AmberTools, so would not be affected
by any upgrade to that part of the code; (b) nmode hasn't changed in
twenty-odd years; (c) running nmode on a protein with 270 residues is indeed
something that could bring nmode to its knees, and I somewhat surprised that
it ever worked.
I don't think we can help without knowing *lots* of details. If you really
want normal modes of large proteins, I would direct you to the nmode()
facility in NAB (or the the python version of MM-PBSA).
...dac
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Received on Thu Sep 22 2011 - 06:30:04 PDT
