[gmx-users] editconf do not center protein

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 29 12:22:04 CEST 2012

On 6/29/12 4:48 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I want to put my protein in a box with the command:
> editconf -f 3m71.gro -o 3m71_box.gro -c -bt dodecahedron -d 1.0 2>>logErr
> 1>>logOut
> and add solvent afterwards with:
> genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro
> 2>>logErr 1>>logOut
> But when I look at it I see that the protein is not in the center of the
> box. Why? There are no errors or warnings in the log files.

The protein is centered, but the representation of the unit cell is probably not 
what you expect.  The box will be represented by a triclinic unit cell unless 
re-wrapped with trjconv -pbc mol -ur compact (which requires a .tpr file).



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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