Re: imaging in amber6

From: David Case <>
Date: Fri 2 Mar 2001 09:05:39 -0800

On Fri, Mar 02, 2001, Riccardo Nifosi wrote:

> am I right that in sander6 output the atoms are not imaged back in the box?
> In my simulation I see water molecules far away from the solute, but I
> suppose they should be imaged back to the box....

This is correct, although it can be modified by the "iwrap" variable. My
recommendation is to keep iwrap=0 in sander, and use ptraj to image the
coordinates back to the primary unit cell. The reason is that ptraj is
more flexible than sander in doing this imaging, so you are more likely to
get exactly what you want.

...good luck....dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Fri Mar 02 2001 - 09:05:39 PST
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