[gmx-users] editconf do not center protein

[Justin A. Lemkul]

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

-- 
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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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