AMBER Archive (2003)

Subject: Re: Sander box error and thanks on previous mdin error

From: David A. Case (case_at_scripps.edu)
Date: Fri Jan 03 2003 - 09:40:07 CST

On Thu, Jan 02, 2003, kxg2248_at_njit.edu wrote:
>
> Here is the error message I get after the restart:

> getting new box info from bottom of inpcrd
> | peek_ewald_inpcrd: Box info not found in inpcrd

This is correct: your restart file does not have any box information in it,
and it should be there. You can check yourself: the box information is
the final line of the file, with 6 numbers (x,y,z and three angles, which
are probably 90.)

But with only 24 atoms in your system, do you really want this to be
periodic? Amber is not designed to handle crystals with very small unit
cells, or otherwise extremely small periodic systems. What is the chemical
system you are simulating? How did you set it up in LEaP, i.e. did you
use the setBox or solvateBox commands?

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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