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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