Hi all,
Well, as described in the manual, the bonded parameters were taken from
Lipid17 (& GLYCAM in tha case of PtdIns), with constrained
mulitconformational charges derived similar to Lipid14, so they should by
all means be compatible. The validation is certainly missing though, which
is why I insist there to be cautious with their use and why they haven't
been published. I will be happy to see Lipid20, so whenever is out
please let me know.
Cheers,
El mar., 5 may. 2020 a las 16:31, Ross Walker (<ross.rosswalker.co.uk>)
escribió:
> 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
> > 80 Wood Lane
> > London W12 0BZ
> >
> >
> >
> > On 05/05/2020, 14:48, "Stephan Schott" <schottve.hhu.de> wrote:
> >
> >
> > *******************
> > This email originates from outside Imperial. Do not click on links
> and attachments unless you recognise the sender.
> > If you trust the sender, add them to your safe senders list
> https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping
> for this address.
> > *******************
> > 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>)
> > escribió:
> >
> >> 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
> > Universitaetsstr. 1
> > 40225 Duesseldorf
> > Germany
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> >
> >
>
>
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--
Stephan Schott V.
Bioquímico / Licenciado en Bioquímica
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Received on Tue May 05 2020 - 08:00:02 PDT
