normal aggregation of proteins in presence of sugar

  • cm
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9 months 3 weeks ago #8843 by cm
I want to calculate proteins aggregation in presence of a certain concentration (M) of sugar by using martini force field. Is there any tutorial to follow. I have already prepared a system consisting of proteins, ions and water by using this tutorial " www.cgmartini.nl/index.php/tutorials-gen...n-gmx5/proteins-gmx5 ". Now my next target is to prepare a system consisting of proteins, ions, water and certain concentration of sugar.

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9 months 3 weeks ago #8844 by vainikka
Replied by vainikka on topic aggregation of proteins in presence of sugar
You can find the Martini 2 sugar topologies here:
cgmartini.nl/images/parameters/ITP/martini_v2.0_sugars.itp

If the list does not contain the specific sugar you are interested in, you will have to a) parameterize it yourself, b) look at the literature and try to find a topology there.

Also be aware that Martini 2 overestimates the strength of protein–protein interactions: pubs.acs.org/doi/10.1021/ct400008p

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5 months 1 week ago #9042 by riccardo
Replied by riccardo on topic aggregation of proteins in presence of sugar
This is totally late but, for future reference, note also that sugar-sugar interactions are overestimated as well in Martini 2: pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00374

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4 weeks 21 hours ago #9222 by JBinder
Replied by JBinder on topic aggregation of proteins in presence of sugar
Hey riccardo,

are there parameterization files for sugars available yet? As you stated the parameters from martini2 lead to unrealistic cluster creation.

Thank you very much
Jonas

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