Re: AMBER: stripping water from a restart file

From: Gustavo Seabra <>
Date: Mon, 27 Oct 2008 13:12:04 -0400

On Fri, Oct 24, 2008 at 5:58 AM, CHAMI F. wrote:
> NMR restraints: Bond = 0.996 Angle = 0.000 Torsion = 0.000
> The system has extended beyond
> the extent of the virtual box.

As the message says, your system somehow got too large, and is outside
the simulation box. this is odd, because (from one of your previous
emails) you are using ntb=0...

Before trying anything else, you should probably look at your system
in some GUI (VMD for example), and see if it's OK. It may be blowing
up for some reason. If you think its OK, then look at your restart
file. From one of your previous e-mails, I see that it ends as:

> [...]
> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> 47.5548619 48.0586172 47.1058278 90.0000000 90.0000000 90.0000000

the last line of the file (second here) is the box information: the
first 3 numbers are sizes, the last 3 are angles. Try just changing
the box size to something larger. Since this is in vacuum, the size of
the box won't matter much anyways, so put something like 90 in all the
numbers there and you should be OK.

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
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Received on Wed Oct 29 2008 - 05:08:03 PDT
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