[gmx-users] editbox removes dummy atoms

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 28 16:17:46 CEST 2012

On 6/28/12 10:11 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I have an protein structure with many dummy atoms around it simulating the
> membrane around the protein. Those dummy atoms are signed in the file as
> an ATOM.
> When I want to put this protein with the membrane in a box with the command
> editconf -f 3m71.gro -o 3m71_box.gro -bt dodecahedron -d 1.0 2>>logErr
> 1>>logOut
> it removes the membrane dummy atoms except of one Dummy atom. How can that
> be.
> What do I have to change?

Does the second line of the .gro file specify the correct amount of atoms?  The 
only reason I know of that editconf will truncate the file is if this line is 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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