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
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Received on Mon Dec 09 2024 - 01:30:03 PST
