From: Ashar Malik (
Date: Sat Jan 18 2020 - 08:37:54 CST

For orienting things you have to work out rotations and translations.

While translations are relatively straightforward, rotations can be tricky
as its hard to visualise especially since a lot of time people want to
rotate about the centre of the molecule but the commands usually rotate
about x, y or z axis which can lead to different results.

A way that I have come to use over the years is to use principle axes ...
so for instance you can calculate the axes of the bilayer and align any of
those axes to x, y and/or z planes.
Then orient the protein (using principle axes if needed) and then translate
to the respective place in the membrane. Then remove any lipids overlapping
with protein. Minimize, equilibrate and follow that with your production.

The package can be found here.

Hope this helps.

On Sat, Jan 18, 2020 at 8:18 PM Yogesh Sharma <>

> hello everyone
> i am trying to orient a protein in bilayer. I have used simulated protein
> pdb for orient. My previous intution based efforts using move residue
> options of vmd failed to provide desired results. I need packed structure
> for further simulation in gromac forcefield. can anyone suggest a reliable
> protein orienting way?