AMBER Archive (2009)

Subject: Re: [AMBER] Nmode "not running properly" problem in MM_PBSA

From: case (case_at_biomaps.rutgers.edu)
Date: Sun Dec 13 2009 - 09:06:36 CST

On Wed, Dec 09, 2009, Du Yun wrote:

> I've got a problem when performing an mm_pbsa calculation with nmode. My
> system has 10080 atoms...

This is a very large system for nmode.

>
> Total memory required : 457748863 real words
> Total memory required : 51440135 integer words

You will need around 4-6 Gbytes of memory to run this job. Do you have that
much available?

> step = 0
> F = 0.299559E+04 GRDMAX = 0.398139E+02 GNORM = 0.279335E+01

You should only be running nmode after minimizing to a small gradient (say
0.0001 kcal/mol-A). Please check that nmode and sander are giving you the
same energies and gradients.

> (the file ends here)

It's possible that the output might be buffered and you have lost the last few
lines.

You may need to consider using the nmode() function in NAB to carry out the
analysis (or, find some alternative way to estimate entropies).

...good luck...dac

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