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 - 00:30:02 PDT
