AMBER Archive (2008)

Subject: Re: Fwd: AMBER: lastrst problem

From: David A. Case (
Date: Tue Mar 18 2008 - 10:37:48 CDT

On Wed, Mar 12, 2008, san_amber roy wrote:
> Dear amber users,
> I am using amber8. I am simulating
> one model peptide solvated with methanol. But here I just wanted one solvate
> methanol, so I used 1.5 angstrom buffer, which added one methanol to the
> model system.
> Now when I am minimizing this total system with sander, I am getting the
> very common following error......
> Exceeding lastrst in get_stack

You are using a 2.5 Ang. cutoff for nonbonded interactions. This will never
work, as you found out. You need to use at least 8 Ang. for periodic systems.
This in turn means that you will probably need to make a bigger box: about
18 Ang. on each side is as low as sander will go.

Admittedly, the error message should be better. Current versions of Amber
would not let you put in such a small cutoff.

...good luck...dac

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