On 7/3/12 5:10 AM, [email protected] 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
--
========================================
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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