Re: [AMBER] entropy calculation failed again!

From: case <>
Date: Sat, 5 Jun 2010 08:03:43 -0400

On Sat, Jun 05, 2010, Rilei Yu wrote:
>  Here is the information I can obtain:
> ----Convergence Satisfied----
> allocation failure in vector: nh = 440496144

If you have 420 residues or so, you will need *lots* of memory. The
allocation above is asking for 440 million words, or over 3 Gbytes of main
memory. The machine you are running on does cannot supply that much.

There is no easy way to solve this problem. Certainly, you shold avoid
running the entire mmpbsa script until you are able to run nmode by hand

I'm hoping(?) that this is not your initial foray into MM-PBSA. To repeat the
usual advice (and add some to it):

1. Be sure you can do these calclations by hand before trying to automate the
process with scripts;

2. Start with small and simple problems, so you have an idea of what sort of
results to expect, and so that problems that inevitably occur are easier to

...good luck....dac

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Received on Sat Jun 05 2010 - 05:30:03 PDT
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