Thanks Dac,
I understood the problem and another reason may be
inhomogenious distribution of solvant molecules.
sincerely,
Santanu
On Tue, Mar 18, 2008 at 4:37 PM, David A. Case <case.scripps.edu> wrote:
> 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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Received on Fri Apr 18 2008 - 21:12:18 PDT
