Re: [AMBER] MMPBSA and membrane effect incorporation for GBSA

From: Ray Luo via AMBER <amber.ambermd.org>
Date: Wed, 3 Jul 2024 14:33:50 -0700

Stéphane,

Thanks for trying out the new membrane features! Regarding your questions,
I don't think you can easily do membrane MMPBSA simulations with setups not
mentioned in the manual or the test cases. Specifically, the new automatic
membrane setup is not for GBSA applications as we do not have a
membrane-dielectric GBSA. In addition, the residue-based decomposition does
not work for membrane MMPBSA. We are working on these features and will
release these in future Amber versions.

All the best,
Ray

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Wed, Jul 3, 2024 at 1:28 AM Stéphane Téletchéa via AMBER <
amber.ambermd.org> wrote:
> Dear all,
>
> I am testing the automated routine for membrane simulations of proteins
> using AMBER24.
> I try to compare GBSA and PBSA evaluations, PBSA being run with the
> automatic incorporation of the membrane
> during calculations (inp=1).
>
> Of source I see large differences in numerical decomposition for some
> amino acids close to the membrane,
> but for many, GBSA and PBSA parameters are close.
>
> My question is thus is there an option to turn on membrane dielectric in
> GBSA?
> Any theoretical or practical reason for this?
>
> Thanks a lot in advance, just wondering, and found no answer in my
> literature search.
>
> 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
>
> https://urldefense.com/v3/__http://www.us2b.univ-nantes.fr/__;!!CzAuKJ42GuquVTTmVmPViYEvSg!PPaBk0UvjM522z9_cRe3HZWLKSMX04oQpWFnRzHQoQMhTl83bJdAvW7_DcIeB28HJaGPAClZw7oypg$
>  -
> https://urldefense.com/v3/__http://www.steletch.org__;!!CzAuKJ42GuquVTTmVmPViYEvSg!PPaBk0UvjM522z9_cRe3HZWLKSMX04oQpWFnRzHQoQMhTl83bJdAvW7_DcIeB28HJaGPACmNYQlZCQ$
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!PPaBk0UvjM522z9_cRe3HZWLKSMX04oQpWFnRzHQoQMhTl83bJdAvW7_DcIeB28HJaGPACn1oXguZw$
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Jul 03 2024 - 15:00:02 PDT