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Difference between alanine and proline
- floris
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2 years 9 months ago - 2 years 8 months ago #9007
by floris
Difference between alanine and proline was created by floris
Hello,
I am doing a set of martini 3 simulations, in which i mutate glycine residues to either alanine or proline residues. I heard that the dihedral and angle potentials in Martini 3 are very preliminary, and i was advised to parametrize them myself.
To get some inspiration, i looked at the martini 2 protein parameters, but i have some problem understanding what is the difference between an alanine and a proline in Martini 2, i expected some difference in angles and dihedrals, but there are virtually no differences. Does any of you know:
1) How the difference in phi/psi angles between alanine and proline are reflected in Martini 2 and 3
2) What is the reason there no dihedral defined between the SC1(n-1)-BB(n-1)-BB(n)-SC1(n) beads, as I think that would somehow capture the phi/psi angle behaviour of the different aminoacids. (I know that the scFIX addition by Herzog et al. defines this dihedral, but if I understand correctly, this has mostly to do with beta sheets?
Thanks for your help/suggestions,
Best,
Floris
I am doing a set of martini 3 simulations, in which i mutate glycine residues to either alanine or proline residues. I heard that the dihedral and angle potentials in Martini 3 are very preliminary, and i was advised to parametrize them myself.
To get some inspiration, i looked at the martini 2 protein parameters, but i have some problem understanding what is the difference between an alanine and a proline in Martini 2, i expected some difference in angles and dihedrals, but there are virtually no differences. Does any of you know:
1) How the difference in phi/psi angles between alanine and proline are reflected in Martini 2 and 3
2) What is the reason there no dihedral defined between the SC1(n-1)-BB(n-1)-BB(n)-SC1(n) beads, as I think that would somehow capture the phi/psi angle behaviour of the different aminoacids. (I know that the scFIX addition by Herzog et al. defines this dihedral, but if I understand correctly, this has mostly to do with beta sheets?
Thanks for your help/suggestions,
Best,
Floris
Last edit: 2 years 8 months ago by floris. Reason: made a mistake in the dihedral definition, was SC1(n-1)-BB(n-1)-BB(n)-BB(n+1)
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