Hi,
Note that as of version 6.29.9 (currently on GitHub) there is a new
experimental keyword for ‘autoimage’ that should work much better for
membrane systems:
autoimage mode byvec
If you get a chance to try it please let me know how it worked for you!
-Dan
On Mon, Dec 9, 2024 at 4:17 AM Stéphane Téletchéa via AMBER <
amber.ambermd.org> wrote:
> Dear all,
>
> Back on this, I think I found a more robust solution.
>
> While looking at the "autoimage" function, it turns out that it took my
> proteins (I have two) + some lipids (like 15 additional ones).
>
> Le 10/03/2024 à 17:46, Daniel Roe via AMBER a écrit :
> > Hi,
> >
> > Try using the moveanchor keyword, which when determining fixed positions
> > uses the previous molecule as an anchor. It’s a bit of a hack but I’ve
> had
> > it work well with membrane systems.
> >
> > -Dan
>
> Instead of using autoimage (which was nearly fine to me), I used the
> proteins residues + all the lipids involved in the upper leaflet:
>
> center ":1-569" mass origin
> image origin center familiar
> center ':PA,PC,OL'
>
> This allows to produce a nice imaged system with all the lipids in the
> correct box, and the protein centered mostly
> in the middle of the membrane, as expected from the starting coordinates.
>
> HTH,
>
> Stéphane
>
> --
> Assistant Professor, USBB, UMR 6286 CNRS, Bioinformatique Structurale
> UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322
> Nantes cedex 03, France
> Tél : +33 251 125 636 / Fax : +33 251 125 632
> http://www.us2b.univ-nantes.fr/ -http://www.steletch.org
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 09 2024 - 05:30:03 PST
