[gmx-users] problems with editconf

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 3 11:33:16 CEST 2012

On 7/3/12 5:10 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I want to put my protein in the box with editconf but when I look at it it
> is always at the border of the box and not at the center. I tried it with
> those two commands:
> editconf -f 3m71.gro -o 3m71_box.gro -center 4.59340   4.59470   5.17330
> -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut
> editconf -f 3m71.gro -o 3m71_box.gro -c -bt dodecahedron -d 1.0 2>>logErr
> 1>>logOut
> With the first command it is at the upper border and with the second
> command it is at the right border. The coordinates of the firs command are
> from the 3m71.gro file.
> Can you please tell me what is wrong?

Nothing.  When visualizing the unit cell, it will appear as a triclinic box with 
the protein in a seemingly random location.  You can re-wrap the unit cell with 
trjconv -pbc mol -ur compact (which requires a .tpr file) to see the 
dodecahedral unit cell with everything placed as you would expect.



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


More information about the gromacs.org_gmx-users mailing list