AMBER Archive (2009)

Subject: Re: [AMBER] box problem

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Aug 13 2009 - 06:50:54 CDT

On Thu, Aug 13, 2009, Nancy wrote:

> I use command set unit box {x y z} in xleap to add a rectangular box
> to my unit,but there is interspace between box and unit ,ir there any
> method that i can add a periodic box to my unit without interspace with
> the unit.

Can you explain more fully what you mean by "interspace between box and unit"?
If you set the box as above, LEaP uses those values, independent of where any
atoms might be located. Are you sure that you have chosen the best values for
x,y and z? Are you sure you want to use that command? What are you trying to
accomplish?

...dac

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