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normal Secondary structure

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10 years 11 months ago #1593 by martini
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HI,

I compute a Martini simulation from an All - atom structure. My structure contains some beta-sheet structure at the beginning but when the martini simulation was done and after convert my "martini structure" to "all atom" structure I lost this secondary structure.
SO I would like to know if with Martini model we lost secondary structure or the simulation happen normally.

THanks a lot .

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10 years 11 months ago #1594 by xavier
Replied by xavier on topic Secondary structure
your user name is rather confusing ... you should know all about martini already! :))

considering the secondary structure in MARTINI ... b-sheets are not stable and ternary/quaternary structures are difficult to preserve in the exact conformation without using the ElNeDyn approach.

martini wrote: HI,

I compute a Martini simulation from an All - atom structure. My structure contains some beta-sheet structure at the beginning but when the martini simulation was done and after convert my "martini structure" to "all atom" structure I lost this secondary structure.
SO I would like to know if with Martini model we lost secondary structure or the simulation happen normally.

THanks a lot .

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10 years 11 months ago #1595 by martini
Replied by martini on topic Secondary structure
LOl true my username Its not a good choice :p

BUt there is no way in Martini to impose kind of constraint for do not lose b-sheet structure??

Thanks a lot

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10 years 11 months ago #1596 by xavier
Replied by xavier on topic Secondary structure
the beta-strands (extended structure) should be conserved with MARTINI but to keep interactions between strands we normally use ElNeDyn.

martini wrote: LOl true my username Its not a good choice :p

BUt there is no way in Martini to impose kind of constraint for do not lose b-sheet structure??

Thanks a lot

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10 years 11 months ago #1597 by martini
Replied by martini on topic Secondary structure
Ok I will try to use ElNeDyn .

Thanks a lot

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