Re: AMBER: nmode entropy estimating problem

From: David A. Case <>
Date: Wed, 22 Sep 2004 13:29:04 -0700

On Wed, Sep 22, 2004, jwfang wrote:

> I use 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

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.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Sep 22 2004 - 21:53:00 PDT
Custom Search