AMBER: overlap problem

From: Ioana Cozmuta <>
Date: Mon, 18 Aug 2003 14:26:57 -0700 (PDT)

Hi amber users,

I want to overlap a box of ionic solution (coresponding to 1MKCL,
previously equilibrated) with a DNA strand. Initially I thought that I can
center both structures in zero, remove the water molecules that overlap
with the DNA strand and here it is my structure of DNA in 1M solution.
However I now realize that if I do that, by removing the water molecules I
am changing the molarity of the solution.
Any suggestion what would be the best way to keep the number of water and
ions constant but still remove the overlaps (minimizing the structure
would not work).

Thank you,

* Ioana Cozmuta, PhD * *
* NASA-AMES Research Center * "Gravitation can not be held responsible*
* Mail Stop 230-3 * for people falling in love" *
* Moffet Field,CA 94035 * *
* phone: (650) 604-0993 * Albert Einstein*
* fax: (650) 604-0350 * (1879-1955) *

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Received on Mon Aug 18 2003 - 22:53:00 PDT
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