From: Andrew Jewett (
Date: Wed Feb 29 2012 - 19:24:10 CST

I have heard Axel recommend PACKMOL for preparing simulations of
protein inclusions:

I hope this helps.

(Packmol and similar programs generate coordinates only and don't
depend on the force-field, phospholipid molecule, or simulation
software you are using.)

On Wed, Feb 29, 2012 at 1:33 PM, Albert <> wrote:
> Hello:
>   I've superimposed my homology models with related OPM protein. And now I
> would like to embed my protein to pre-equilibrated membrane POPE from
> But I found that the position is not correct for the membrane.... Does
> anybody have any idea how to do it? I am going to use CHARMM36 based POPE
> for my aligned protein.