Thank you very much Foley for your details discussion.
Thank you Anselm for your help. I will go through your paper and let you
know.
On Tue, 27 Aug 2019, 13:01 Horn, Anselm, <anselm.horn.fau.de> wrote:
> Dear Rajarshi,
>
> we recently investigated the interaction of a protein with trehalose acyl
> esters bearing alkane chains of different length. In the supplement of our
> work we provided a rather detailed description of the parameterization.
> Maybe this could be of interest for you:
> https://doi.org/10.1038/s41598-018-23624-8
>
> Best regards,
>
> Anselm
>
>
> ________________________________________
> Von: Lachele Foley <lf.list.gmail.com>
> Gesendet: Samstag, 24. August 2019 22:17
> An: AMBER Mailing List
> Betreff: Re: [AMBER] Glycolipid Simulation
>
> You should be able to use both force fields: glycam and lipid. I'm
> sure this has been done before, too. Search this list or the
> literature for examples.
>
> We haven't done any glycolipid simulations in the group since our
> (much older) release of a lipid force field. There is information
> about that in the AMBER manual. Disclaimer: I am not a biochemist,
> but... I think you should be able to just attach a glycan to a head
> group in the lipid ff. For setting parameters that span the force
> fields, you probably want anything containing the glycan and the
> glycosidic O (even if the O originates in the lipid) to come from the
> glycam parameters as much as possible. This is because the glycam
> params will help ensure certain geometric properties specific to
> glycans.
>
> Let me know if you have any questions. I realize this isn't a deep
> answer, but it might be all you need.
>
> On Fri, Aug 23, 2019 at 8:08 AM Rajarshi Roy <phd1701171011.iiti.ac.in>
> wrote:
> >
> > Dear AMBER users and developers,
> > I want to simulate protein and glycolipid complex such as
> > phosphatidylinositol or GM1. I am not aware of how to prepare a topology
> > file for the glycolipid molecules. Does it possible to make it using
> glycam
> > force field only? Alternatively, Can I use lipid forcefield? Is there any
> > tutorial or scripts available from which I can start?
> > Any help will be highly appreciated.
> > Thank you!
> > --
> > *with regards*
> >
> > *Rajarshi Roy*
> >
> >
> > *PhD Research Scholar*
> >
> > *Biosciences and Biomedical Engineering*
> >
> > *Indian Institute of Technology, Indore*
> > *India*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Tue Aug 27 2019 - 04:30:02 PDT
