[gmx-users] protein in hole

[gportel at gwdg.de]

Hi,

Use editconf. You can center the protein and align its main axis ( -princ
) or play around with the rotation of the initial orientation ( -rotate ).
Then get the surface of the correct (aligned and centered) oritentation as
input for making the hole (if you want to use the modified md code).

Good luck,

Guillem


---------

Guillem Portella
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
D-37077 Göttingen
Germany


>  Dear all
> i want to insert potassium channel in popc, i made
> popc+hole by make-hole but i can not to insert protein
> in popc, i merg the coordinates of the protein and the
> lipid bilayer in a single file, the protein turns out
> not to be inside the hole. I  have to orient the
> protein so that the channel axis coincides with the
> membrane normal.how can i do it by editconf or grasp?
> thanks
>
>
>
>
>
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