AMBER Archive (2009)

Subject: Re: [AMBER] SANDER BOMB in subroutine nonbond_list

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Jun 23 2009 - 11:54:30 CDT

> about 1200 Aminoacid residues and 53000 water molecules
> * NB pairs 91990767 exceeds capacity ( 2062076) 0
> *check MAXPR in locmem.f *
>
> My input file looks like:
> ...ncyc=10000, cut=12.0,ntpr=1000, drms=0.001
> Can anybody please point out where I am going wrong and how to fix it ?

You could drop your cutoff to 8A (minimization is so crude a method
that even 4A would suffice to relax for starting dynamics). 8A might
be ok for dynamics too. Or you could "check MAXPR in locmem.f", and
increase it. I would run with 8A or 9A cutoff to get faster speed,
and it still may be necessary to increase MAXPR & recompile.

Bill

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