[AMBER] Shifting molecules by a box length

From: Heribert Reis <hreis.eie.gr>
Date: Wed, 9 Oct 2013 17:53:29 +0300


>From a colleague I got the cartesian coordinates of a snapshot from a
AMBER-MD run of a protein molecule surrounded by water, which I would like
to use now in a different program. I just need the protein molecule, fully
surrounded by a layer of water. In the snapshot the protein molecule is not
fully inside the unit cell (sticking out in z-direction), so I need to
shift some of the water molecules by one box length, but however I do that,
I end up with much too short distances between some of the shifted water
molecules and atoms of the protein.

The unit cell is a truncated octahedron, the triclinic cell length is about
97 Ang (in all 3 directions), so according to some previous messages in
this list, I multiply this by sqrt(3)/2 to get the cubic box length of ~112
Ang (which is also about the max distance between the water molecules in
z-direction, so that seems to be about correct), but just adding this
number to the z-coordinates of the waters I end up with those very short
distances, so I guess that is not the correct procedure. What would be the
correct way to do it?

Best regards,
AMBER mailing list
Received on Wed Oct 09 2013 - 08:00:04 PDT
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