[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
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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