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mapping for cholesterol
- mferraro
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10 years 10 months ago #1701
by mferraro
mapping for cholesterol was created by mferraro
Hi there,
I' ve read all papers referring to the mapping strategy for cholesterol. I've tried to attribute atoms to beads from the figure which represents beads with spheres, but I find this procedure quite confused. I know that the "S" particle type is used for 3:1 mapping in cholesterol rings but there are a lot of ways in which I can combine atoms; indeed I'm not sure that S type excludes the possibility to consider 4 atoms in a ring-bead.
I know from literature (Rzepiela) that a mixed DPPC/CHOL bilayer has been studied for reverse mapping, but CHOL.itp with [ mapping ] section is not provided with tutorial.
Could you kindly suggest me a non ambiguous method to generate this section in my topology?
I will be very grateful to anybody could help me.
Regrets.
Maria.
I' ve read all papers referring to the mapping strategy for cholesterol. I've tried to attribute atoms to beads from the figure which represents beads with spheres, but I find this procedure quite confused. I know that the "S" particle type is used for 3:1 mapping in cholesterol rings but there are a lot of ways in which I can combine atoms; indeed I'm not sure that S type excludes the possibility to consider 4 atoms in a ring-bead.
I know from literature (Rzepiela) that a mixed DPPC/CHOL bilayer has been studied for reverse mapping, but CHOL.itp with [ mapping ] section is not provided with tutorial.
Could you kindly suggest me a non ambiguous method to generate this section in my topology?
I will be very grateful to anybody could help me.
Regrets.
Maria.
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- djurre
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10 years 10 months ago #1702
by djurre
Replied by djurre on topic mapping for cholesterol
Assuming you use a gromos based cholestrol, the mapping would be approximately like this (first column= gromos atom name, second column = martini bead name):
C1 R1
C2 R1
C3 R1
C4 ROH
C5 ROH
O6 ROH
H ROH
C8 ROH
C9 R1
C10 R2
C11 R2
C12 R2
C13 R3
C14 R3
C15 R3
C16 R5
C17 R5
C18 R4
C19 R4
C20 R4
C21 R5
C22 C1
C23 C1
C24 C1
C25 C1
C26 C2
C27 C2
C28 C2
C29 C2
C1 R1
C2 R1
C3 R1
C4 ROH
C5 ROH
O6 ROH
H ROH
C8 ROH
C9 R1
C10 R2
C11 R2
C12 R2
C13 R3
C14 R3
C15 R3
C16 R5
C17 R5
C18 R4
C19 R4
C20 R4
C21 R5
C22 C1
C23 C1
C24 C1
C25 C1
C26 C2
C27 C2
C28 C2
C29 C2
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- mferraro
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10 years 10 months ago #1703
by mferraro
Replied by mferraro on topic mapping for cholesterol
Great, Djurre!
Thank you very much!
I think it will be so useful to many Martini-users!
Thank you very much!
I think it will be so useful to many Martini-users!
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