AMBER Archive (2006)

Subject: Re: AMBER: non bond list overflow

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 07 2006 - 00:37:59 CST

On Mon, Feb 06, 2006, Kenley Barrett wrote:
>
> I recently tried to run a minimization of a large system (about 12000 heavy
> atoms in the solute and then about 30000 water molecules). The minimization
> stopped with the following error:
>
> * NB pairs 191 17999833 exceeds capacity ( 18000000) 0
> SIZE OF NONBOND LIST = 18000000
> EWALD BOMB in subroutine ewald_list
> Non bond list overflow!
> check MAXPR in sizes.h
>
> I looked for the sizes.h file in $AMBERHOME/src/sander and couldn't find it.

I guess we need to know what version of Amber you have or are running.
Amber 7 is the last version that had the error message "check MAXPR in
sizes.h", and it *does* have a sizes.h file in amber7/src/sander.

Amber 8 does not have either the error message, nor the sizes.h file.

Is it possible that you are running an executable verison of amber7, but that
$AMBERHOME points to the source code for Amber 8? Other than that, I can't
really think how the situation you describe could happen. [Doesn't mean that
it can't/didn't happen some other way...it may just be my lack of imagnation.]
If this doesn't help, let us know which version you are using.

...regards...dac

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