VMD-L Mailing List

From: Andrew Jewett (jewett.ai_at_gmail.com)
Date: Wed Feb 29 2012 - 19:24:10 CST

I have heard Axel recommend PACKMOL for preparing simulations of
protein inclusions:
http://www.ime.unicamp.br/~martinez/packmol/

I hope this helps.

Andrew
(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 <mailmd2011_at_gmail.com> 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
>
>  http://terpconnect.umd.edu/~jbklauda/research/download.html
>
> 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.
>
> THX