Darn. I was hoping that would work a bit better. One of the current issues
is that the code still needs the first frame to look “nice” (i.e. how you
want it to look).
If you could send me the files off list I would be grateful. The more
examples I have the better!
Thanks,
-Dan
On Tue, Dec 10, 2024 at 9:30 AM Téletchéa Stéphane via AMBER <
amber.ambermd.org> wrote:
> Le 09/12/2024 à 14:08, Daniel Roe via AMBER a écrit :
> > 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
> Tried the latest version available (your commit from December 6th), and :
> (a) good news, the protein is correctly packed AND at the center of the
> lipids
> (b) good news, the lipids do not jump from one box to the other like
> they do on autoimage alone
> (c) bad news, the lipids are in a much bigger box (xy plane is fine), so
> the membrane seems porous (see screenshot).
>
> I can share off the list the files and more details if you wish to have
> a benchmark.
>
> Best,
>
> Stéphane
>
> --
> Maître de conférences Hors Classe, PEDR, HDR
> US2B, Nantes Université, CNRS, UMR 6286, Team Structural Bioinformatics,
> F-44000 Nantes
> http://www.us2b.univ-nantes.fr/ - http://www.steletch.org
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Received on Wed Dec 11 2024 - 06:30:03 PST
