AMBER Archive (2007)

Subject: Re: AMBER: Non bond list overflow

From: David A. Case (case_at_scripps.edu)
Date: Sun Jul 15 2007 - 18:50:11 CDT

On Sat, Jul 14, 2007, neville forlemu wrote:

> This is the very first time that i am using amber8, and got into trouble
> while trying to minimized my molecule.
> however got this error.
> Was wondering whether u could help me out
>
>
> NB pairs 7955 136753434 exceeds capacity ( 136754557) 0
> SIZE OF NONBOND LIST = 136754557
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
>

We need more information. How big is you system? Is it a periodic
simulation? Have you looked at the coordinates visually to ensure that the
molecule/solvent look OK?

This is an error is not supposed to happen. There can be a variety of
causes, but the most common is that the input coordinates are bad. If you
can't see anything by looking at the structure in a graphics program like VMD,
you might want to post how you created the prmtop and coordinate files.

Since you say it is your first time, working through tutorial B1 (if you have
not already done so) would be a good idea. Maybe that will show you where the
problem lies.

...regards....dac

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