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normal How is charge distributed for polar amino acids in polarisable MARTINI model

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4 years 4 months ago #8354 by wuzhiyi
How is charge distributed for polar amino acids in polarisable MARTINI model was created by wuzhiyi
In the script martinize.py, if the polarisable force field option is selected, the polar amino acid residues will have dummy beads with the opposite charge to reflect the polarity of the amino acids.
For example, glutamine has two beads with charge 0.42 and -0.42, while asparagine has two beads with charge 0.46 and -0.46. The serine has two beads of 0.4 and -0.4, while threonine has two beads of 0.36 and -0.36.
I wonder where can I find the publication which explains how are these numbers derived. I have P3 bread which represents the carboxylic acid group and I wonder what is the best way to distribute the charges so as to replicate the polarity of carboxylic acid.

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4 years 4 months ago #8355 by peterkroon
Replied by peterkroon on topic How is charge distributed for polar amino acids in polarisable MARTINI model
dx.doi.org/10.1021/ct300646g is the Martini 2.2P paper. I only glossed over, but it should contain what you need.

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  1. Force Fields
  3. Proteins
  5. How is charge distributed for polar amino acids in polarisable MARTINI model
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