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exact mapping of cholesterol molecule
- initram
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9 years 10 months ago - 9 years 10 months ago #3852
by initram
exact mapping of cholesterol molecule was created by initram
Hi,
I can't find exact mapping from all atom cholesterol to CG Martini.
Does anyone know exact mapping, in other words what goes to SP1,SC1,SC3,SC1,SC1,SC1,SC1, and C1?
I think that it would be good practice to have exact mapping available in the topology file.
Thank you.
I can't find exact mapping from all atom cholesterol to CG Martini.
Does anyone know exact mapping, in other words what goes to SP1,SC1,SC3,SC1,SC1,SC1,SC1, and C1?
I think that it would be good practice to have exact mapping available in the topology file.
Thank you.
Last edit: 9 years 10 months ago by initram.
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- Clement
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9 years 10 months ago #3859
by Clement
Replied by Clement on topic exact mapping of cholesterol molecule
What if there's no "official" mapping to it? I believe a suggestion can be found in the Backward tool directory, but doesn't have to be it. Mapping for cholesterol, due to the multiple rings structure, is quite hard to define...
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- initram
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9 years 10 months ago #3864
by initram
Replied by initram on topic exact mapping of cholesterol molecule
Hi Clement,
Thank you for your answer.
In the paper "The Martini Force Field: Coarse Grained Model for Biomolecular Simulation" I see that "several different geometries for cholesterol" were tested and a model from the Figure 1. is the one that author adopted. Even more, very helpful Table 2 is given, but the borders between beads in Figure 1 are not clear. I see overlaps between different beads and that makes me hard to figure out the real mapping. I know that I could probably start with any mapping but I would really like to use the one from the paper.
Thank you again
Thank you for your answer.
In the paper "The Martini Force Field: Coarse Grained Model for Biomolecular Simulation" I see that "several different geometries for cholesterol" were tested and a model from the Figure 1. is the one that author adopted. Even more, very helpful Table 2 is given, but the borders between beads in Figure 1 are not clear. I see overlaps between different beads and that makes me hard to figure out the real mapping. I know that I could probably start with any mapping but I would really like to use the one from the paper.
Thank you again
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- Marie-Ange
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9 years 10 months ago #3867
by Marie-Ange
Replied by Marie-Ange on topic exact mapping of cholesterol molecule
Hi Initram,
In the paper you quote, I deduced the topology of cholesterol by the figure 1 also. I try the mapping like I show in another post (Cholesterol and beads for NAMD use). You can see the mapping for cholesterol and a proposed answer for topology to the end.
If you disagree with the design, do not hesitate to say so.
In the paper you quote, I deduced the topology of cholesterol by the figure 1 also. I try the mapping like I show in another post (Cholesterol and beads for NAMD use). You can see the mapping for cholesterol and a proposed answer for topology to the end.
If you disagree with the design, do not hesitate to say so.
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- initram
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9 years 10 months ago - 9 years 10 months ago #3884
by initram
Replied by initram on topic exact mapping of cholesterol molecule
Bingo!
I independently mapped cholesterol this morning and I got the same topology as you did. Now, this is encouraging for me, but I have to say that I am not an expert in Martini FF and I can't confirm that this is 100% correct and it looks to me that it differs from this post: "mapping for cholesterol" ( md.chem.rug.nl/cgmartini/index.php/forum...ping-for-cholesterol )
Here is my mapping:
chol; type; atom
C2; SP1; ROH
H2A
H2B
C3
H3
O3
H_(O3)
C4
H4A
H4B
C1; SC1; R1
H1A
H1B
C5
C10
C19
H19A
H19B
H19C
C6; SC3; R2
H6
C7
H7A
H7B
C8
H8
C9; SC1; R3
H9
C11
H11A
H11B
C12
H12A
H12B
C14; SC1; R4
H14
C15
H15A
H15B
C16
H16A
H16B
C13; SC1; R5
C18
H18A
H18B
H18C
C17
H17
C20; SC1; C1
H20
C21
H21A
H21B
H21C
C22
H22A
H22B
C23
H23A
H23B
C24; C1; C2
H24A
H24B
C25
H25
C26
H26A
H26B
H26C
C27
H27A
H27B
H27C
Thanks
I independently mapped cholesterol this morning and I got the same topology as you did. Now, this is encouraging for me, but I have to say that I am not an expert in Martini FF and I can't confirm that this is 100% correct and it looks to me that it differs from this post: "mapping for cholesterol" ( md.chem.rug.nl/cgmartini/index.php/forum...ping-for-cholesterol )
Here is my mapping:
chol; type; atom
C2; SP1; ROH
H2A
H2B
C3
H3
O3
H_(O3)
C4
H4A
H4B
C1; SC1; R1
H1A
H1B
C5
C10
C19
H19A
H19B
H19C
C6; SC3; R2
H6
C7
H7A
H7B
C8
H8
C9; SC1; R3
H9
C11
H11A
H11B
C12
H12A
H12B
C14; SC1; R4
H14
C15
H15A
H15B
C16
H16A
H16B
C13; SC1; R5
C18
H18A
H18B
H18C
C17
H17
C20; SC1; C1
H20
C21
H21A
H21B
H21C
C22
H22A
H22B
C23
H23A
H23B
C24; C1; C2
H24A
H24B
C25
H25
C26
H26A
H26B
H26C
C27
H27A
H27B
H27C
Thanks
Last edit: 9 years 10 months ago by initram.
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- Marie-Ange
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9 years 10 months ago - 9 years 10 months ago #3887
by Marie-Ange
Replied by Marie-Ange on topic exact mapping of cholesterol molecule
The link is for a topology in gromos, I used another definition for numbers of atoms (
eatingacademy.com/wp-content/uploads/2012/04/Cholesterol.gif
). In gromos, the numbers begin at CH3(19 for us) is CH3(1), CH(10) is CH(2), C(1) is C(3) ...
So, we are :
(beads in gromos) numbers in gromos -> numbers in official nomenclature
(ROH) C4/C5/C8/O6/H7 -> C2/C3/C4/O3/H3
(R1) C1/C2/C3/C9 -> C19/C10/C1/C5
(R2) C10/C11/C12 -> C6/C7/C8
(R3) C13/C14/C15 -> C9/C11/C12
(R4) C18/C19/C20 -> C14/C15/C16
(R5) C16/C17/C21 -> C13/C17/C18
(C1) C22/C23/C24/C25 -> C20/C21/C22/C23
(C2) C26/C27/C28/C29 -> C24/C25/C26/C27
Which is reassuring: the mapping of cholesterol, for the post you mention and us, is exactly the same. I just compare this morning with this : lipidbook.bioch.ox.ac.uk/version/downloa...file/cholesterol.itp
I am not a specialist for MARTINI but it seems ok.
marie-ange.angladon at unamur.be
So, we are :
(beads in gromos) numbers in gromos -> numbers in official nomenclature
(ROH) C4/C5/C8/O6/H7 -> C2/C3/C4/O3/H3
(R1) C1/C2/C3/C9 -> C19/C10/C1/C5
(R2) C10/C11/C12 -> C6/C7/C8
(R3) C13/C14/C15 -> C9/C11/C12
(R4) C18/C19/C20 -> C14/C15/C16
(R5) C16/C17/C21 -> C13/C17/C18
(C1) C22/C23/C24/C25 -> C20/C21/C22/C23
(C2) C26/C27/C28/C29 -> C24/C25/C26/C27
Which is reassuring: the mapping of cholesterol, for the post you mention and us, is exactly the same. I just compare this morning with this : lipidbook.bioch.ox.ac.uk/version/downloa...file/cholesterol.itp
I am not a specialist for MARTINI but it seems ok.
marie-ange.angladon at unamur.be
Last edit: 9 years 10 months ago by Marie-Ange.
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- initram
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9 years 10 months ago #3889
by initram
Replied by initram on topic exact mapping of cholesterol molecule
Hi Marie,
I rechecked mapping from the previous post and you are right, I omitted one atom in the list (C9 -> R1).I guess we have exact mapping now.
By the way, I think that a lot of people in future will benefit from your explanations and conversions.
Cheers
I rechecked mapping from the previous post and you are right, I omitted one atom in the list (C9 -> R1).I guess we have exact mapping now.
By the way, I think that a lot of people in future will benefit from your explanations and conversions.
Cheers
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- Clement
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9 years 10 months ago #3890
by Clement
Agreed.
Thanks to have kept this feed alive! Merci Marie-Ange for your input. And thanks both of you for the demonstration of how wrong I was: coming up with the same mapping proves it isn't so hard to define after all...
I think I'm going to suggest a page on the website with such mappings... Recipe, explanations and examples.
Replied by Clement on topic exact mapping of cholesterol molecule
initram wrote: By the way, I think that a lot of people in future will benefit from your explanations and conversions.
Agreed.
Thanks to have kept this feed alive! Merci Marie-Ange for your input. And thanks both of you for the demonstration of how wrong I was: coming up with the same mapping proves it isn't so hard to define after all...
I think I'm going to suggest a page on the website with such mappings... Recipe, explanations and examples.
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- Marie-Ange
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9 years 10 months ago #3894
by Marie-Ange
Replied by Marie-Ange on topic exact mapping of cholesterol molecule
I am pleased to see that the mapping is correct, without this post I would never have been sure that the cholesterol that I use is right. Thanks you Initram and Clément.
It would be a good idea to put examples of mapping of molecules to help mapping of new molecules by users according to their needs.
marie-ange.angladon at unamur.be
It would be a good idea to put examples of mapping of molecules to help mapping of new molecules by users according to their needs.
marie-ange.angladon at unamur.be
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