normal Secondary structure analysis with MARTINI

  • gypsy
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2 years 2 weeks ago #8601 by gypsy
Dear Martini users,

I just started using Martini and I would like to know the differences between the two versions of Martini: 2.1 and 2.3.
I am running simulations of different peptide sequences (length roughly 20 AA) containing Arg and Trp residues mostly. I used the same parameters for minimization/equilibration/dynamic steps. I changed only the epsilon_r value (15 with Martini 2.1 and 2.5 with Martini 2.3) and the type of water (W with Martini 2.1 and PW with Martini 2.3). I obtained pretty different AP values from SASA, with Aggregation Propensity higher in the case of Martini 2.1. I was expecting the reverse since 2.3 should be more suitable for cation-pi interactions.

Thanks in advance for your help!

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2 years 2 weeks ago #8607 by riccardo
Replied by riccardo on topic Secondary structure analysis with MARTINI
From Hanif - first author of the Martini 2.3P paper ( pubs.acs.org/doi/abs/10.1021/acs.jctc.9b01194 ):

"MARTINI 2.3P does not have ARG and TRP cation-pi interactions. It has choline-aromatics cation-pi interactions. The closest analogue is methylated lysine."

We suggest also to check out the 2.3P paper in more detail.

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2 years 2 weeks ago #8609 by gypsy
Replied by gypsy on topic Secondary structure analysis with MARTINI
Thank you very much Riccardo!

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11 months 1 week ago #9079 by neetusingh
Replied by neetusingh on topic Secondary structure analysis with MARTINI
I am new to MARTINI. Wants to know that how can we calculate secondary structure content in the MARTINI coarse grained peptides/proteins?

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