Re: [AMBER] The lipid section in the 2020 manual require updating

From: Gould, Ian R <i.gould.imperial.ac.uk>
Date: Tue, 5 May 2020 14:19:50 +0000

Dear All,

Callum, Ross and I are putting together our Lipid 20 paper that includes anionic lipids, poly-unsaturated (PUFA) lipids and sphingomyelin. Head group torsion parameters are revised, resulting in improved agreement with NMR order parameters, and hydrocarbon chain parameters are updated, allowing a better match with phase transition temperatures. I do not know the origin or the mechanism of parameterisation of the lysophospholipids, PtdIns, and cardiolipins that are mentioned in the AMBER 20 manual packmol-memgen package and so cannot give any comment on their suitability for use with the rest of the Lipid 14/17 force fields.
I think that it would be very sensible that the documentation be updated to reflect this information.

Cheers,
Ian

"Education: that which reveals to the wise, and conceals from the stupid, the vast limits of their knowledge."
Mark Twain

 
Professor Ian R Gould, FRSC.
Professor of Computational Chemical Biology
 
Department of Chemistry
Imperial College London
Exhibition Road
London
SW7 2AY
 
MSRH
Imperial College White City Campus
80 Wood Lane
London W12 0BZ
 


´╗┐On 05/05/2020, 14:48, "Stephan Schott" <schottve.hhu.de> wrote:

    
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    Hi Zhiyi,
    The parameters were added as part of the packmol-memgen package. I didn't
    add them to the general force field description, because it could mislead
    people to think that they can be used with the CHARMM-GUI/Lipid14 tutorial,
    which is not the case. Please take a look at that section, and if you have
    questions, let me know.
    Cheers,
    
    El mar., 5 may. 2020 a las 15:10, David A Case (<david.case.rutgers.edu>)
    escribi├│:
    
> On Tue, May 05, 2020, Zhiyi Wu wrote:
>
> >In the change-log, it is said that
> >Lipid17 extended to lysophospholipids, PtdIns, and cardiolipins
> >However, in the amber 2020 reference manual, the lipid section has not
> >been updated to reflect this.
>
> Thanks for the note; it does indeed look like the "new features" list is
> incorrect. I'll get that fixed. It's possible that we may be able to
> add these as an update soon.
>
> ...dac
>
>
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    Stephan Schott Verdugo
    Biochemist
    
    Heinrich-Heine-Universitaet Duesseldorf
    Institut fuer Pharm. und Med. Chemie
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Received on Tue May 05 2020 - 07:30:02 PDT
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