On 6/29/12 4:48 AM, reising...@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

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================


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