Re: AMBER: What does this mean .. ?

From: Carlos Simmerling <>
Date: Thu, 31 Mar 2005 14:33:25 -0500

go to and find the search box to search
the archives (or just go to google, that workds too).
then search for the error message. you'll find out that this has
been discussed many times in the archive.

in general, it's much faster to search the archive rather than waiting
for people to (maybe) reply to your questions. then ask when
you can't find the answer in the archive.
good luck!

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

Pavan Ghatty wrote:

>Amber users,
>I used an .inpcrd and .prmtop file to create two .out
>files during minimization using two input files. There
>was no problem with the first .out file, however after
>altering the .in file, I encountered the following
>problem after running sander for minimization.
>Altered Input file:
>maxcyc = 5000,
>ncyc = 250,
>ntb = 1,
>igb = 0,
>cut = 12
>$ tail w.out
>| CHECK d/dx switch(x): max rel err = 0.7380E-11
>at 2.712360
> ---------------------------------------------------
>| Local SIZE OF NONBOND LIST = 17174632
> Exceeding lastrst
> lastrst = 2000000
> top_stk= 1927494
> isize = 163776
> request= 2091270
> Increase lastrst in the &cntrl namelist
>Please help me understand what each of the terms in
>the error message mean. I did not restart any run. So,
>why does "lastrst" come in to picture...? What is
>NONBOND LIST..? top_stk.. isize. request...?
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Received on Thu Mar 31 2005 - 20:53:01 PST
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