[gmx-users] center of box protein

nahren manuel meetnahren at yahoo.com
Tue Aug 2 16:32:16 CEST 2011

Dear GMX users,

I am trying to center my protein at the center of box using editconf. When I view the same using ngmx, the protein seems to lie outside the box

neweditconf -f alapdb.pdb -bt cubic  -o boxpdb.pdb -c -center -0.156 -0.061 0.084 -d 1.5

this one works, but the molecule is shifted.

neweditconf -f alapdb.pdb -bt cubic -d 1.5 -o try.pdb

I want my molecule (geometrical )  center to be the center of the box with -d 1.5.

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