On Wed, Sep 22, 2004, jwfang wrote:
> I use mm_pbsa.pl to evaluate the binding free energy for ligand to a 860 AA
> protein (16000 atoms). The problem is I have not been able to get nmode to
> estimate entropy work.
There is no ordinary way that you can use Amber to do a normal mode
calculation on such a large system. It would take over 9 GBytes of memory
just to store the Hessian. You could try setting ismem=1, but it is likely
that you will have to write your own specialized code to handle such big
systems.
I think we have actually done some systems approaching 8,000 atoms, on true
64-bit machines/compilers. But memory goes like N**2 and computation time
like N**3, so you are talking about a project that this nearly an order of
magnitude more difficult than anything we have ever done.
....dac
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Received on Wed Sep 22 2004 - 21:53:00 PDT
