From: Ross Walker <>
Date: Wed, 8 Sep 2004 07:42:53 -0700

Dear Helios
What cut off are you using? And what do you mean by the comment "it can't
seem more than 7200000" what happens if you set it higher than this?
What version of sander is this btw? Amber 7?
Can you post your input file please? Try reducing the size of your cutoff so
the pair list is smaller. Also try setting maxpr to 10,000,000 and recompile
and then let me know exactly what the error is.
All the best
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |


From: [] On Behalf Of
Sent: 08 September 2004 05:18
Subject: AMBER: Amber: BOMB

Dear all, I am minimizing a protein with ~15984 atoms (included water
molecules) on SGI system (CPU:1*350MHz, Main Memory:256Mb, Swap:128Mb).
When running with sander, after five
seconds or so, the calculation always crashes, and the output is this:

* NB pairs 15525 7199515 exceeds capacity ( 7200000)
      SIZE OF NONBOND LIST = 7200000
  EWALD BOMB in subroutine ewald_list
  Non bond list overflow!
  check MAXPR in sizes.h

I have increased the value for MAXPR already, and it can't seem more than
7200000. Does this question could be solve if I buy more memory (e.g.,
512MB) or any parameters I need to correct?
p.s. When I use "unlimit datasize" command, it happens "Unlimit: datasize:
Can't remove limit".

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Received on Fri Sep 10 2004 - 13:25:59 PDT
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