AMBER Archive (2004)

Subject: Re: AMBER: mm_pbsa.pl nmode entropy estimating problem

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 22 2004 - 15:29:04 CDT

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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