Re: AMBER: simulating a crystal using the unit cell

From: Joseph Nachman <>
Date: Thu, 14 Aug 2003 12:01:34 -0400 (EDT)

Hi -

Amber can't reproduce crystallographic symmetry, so the only way to
simulate yuor crystal is to generate the complete unit cell from ths
asymetric unit (you can do this in O, for instance, by genetrating the
symmetry mates of your pdb coordinates, and writing out the coordiantres
fo those mates that together wiht your original coordinates will make up
the complete unit cell). You than concatenate the original coordinates
with the generated ones, and use this as the input in LeAP, and you
specify the dimensions of the crystallographic unit ccell as your box

Hope this helps,


On Thu, 14 Aug 2003, Sarah Wittkopp wrote:

> Hi,
> I am trying to simulate a crystal, where all atoms are not contained in
> one unit cell. As a result, since the simulation is periodic I thought
> the atoms outside of the box would be imaged in the other side. I think
> the problem lies in that one cannot image all molecules in the unit cell.
> I would like to know if it is possible to alter the imaging in sander
> (AMBER 7) so it can be via atom rather than molecule, (which might be the
> problem?).
> The NPT simulation does run when starting with a box size which contains
> all molecules, and the structure has been checked.
> I have tried starting with the crystal coordinates where some atoms
> remained outside the box and recieved the following error.
> EWALD BOMB in subroutine ewald_list
> volume of ucell too big, too many subcells
> list grid memory needs to be reallocated, restart sander
> (Both PRESS, VIRIAL, and VDWAALS are way too large as well)
> The same error was recieved when I tried two additional simulations, one
> where the coordinates were imaged using ptraj by molecule and the other
> was imaged by atom.
> Thanks in advance for any help,
> Sarah
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Joseph Nachman				Department of Biochemistry		University of Toronto
					Medical Sciences Building
tel: +1 416 978-5510			Toronto, Ontario M5S 1A8
fax: +1 416 978-8548			Canada
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Received on Thu Aug 14 2003 - 17:53:01 PDT
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