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

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 5 May 2020 10:30:23 -0400

I concur. I very much doubt any of that additional parameterization has been tested for compatibility with the existing lipid force fields.

I would advise waiting for Lipid 20 which we will release shortly.

All the best
Ross

> On May 5, 2020, at 10:19, Gould, Ian R <i.gould.imperial.ac.uk> wrote:
>
> 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
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>
>
> ´╗┐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
>
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Received on Tue May 05 2020 - 08:00:02 PDT
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