AMBER Archive (2004)

Subject: Re: AMBER: sander of AMBER 8 doesn't work

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 02 2004 - 09:47:20 CDT

On Wed, Jun 02, 2004, Feng, Hanqiao (NIH/NCI) wrote:

> Thank you very much for your response to my question. Actually, I am using
> NIH Biowulf cluster where AMBER 8 was installed. From .out file, I got the
> error message as:
> * NB pairs 2781 13482275 exceeds capacity(13482333 ) 0
> size of nonbond list = 13482333
> Sander bomb in subroutine nonbond_list
> Non bond list overflow
> Check MAXPR in locmem.f
> Since I have no permission to do the test or any change on the
> superdirectory.

This error should not happen, and probably indicates that something else is
wrong with your system (perhaps with its density). Since you don't say
anything about the nature of your system, it's hard to be more helpful than
that.

You should look in locmem.f to see how MAXPR is calculated. That might offer
some clue. And, you should probably ask to get your own copy of the code
so that changes could be made if necessary. But my guess is that something
is amiss with your input file or the system you are simulating.

...good luck...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu