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normal Backmapping an α-linolen chain with only 4 beads

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8 years 5 months ago - 8 years 5 months ago #5195 by Stéfane
Backmapping an α-linolen chain with only 4 beads was created by Stéfane
Dear All

I currently building a CHARMM36 mapping scheme for PPT* in plant thylakoide membrane. In the van Eerden BBA (2015) paper the authors use a CG model with only 4 beads for the C18 acyl chain. Since I am a newbie in the CG-->AA transformation, i am using the different examples in the Mapping directory downloaded from the martini website to constuct my own maps. In case of the PC with C18 acyl chains, all the models (for instance POPG) used five beads, therefore I am confused how choose the correct mapping scheme when a CG model with only 4 beads.

* (;phosphatidyl-glycerole (PG), with a trans-3-hexadecenoic acid tail (sn1) and an α-linolenoyl tail (sn2) -- 16:1(3t)-18:3(9,12,15) PG)

Thanks again for your insights

Stéfane
Last edit: 8 years 5 months ago by Stéfane.

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8 years 5 months ago #5196 by tsjerk
Replied by tsjerk on topic Backmapping an α-linolen chain with only 4 beads
; Hi Stéfane,

; The correct mapping scheme is the one that works :)
; Here is the .map for POPC for charmm36 from 4-bead tails:

; latest revision kri 12.3.2013
[ molecule ]
POPC

[ martini ]
NC3 PO4 GL1 GL2 C1A D2A C3A C4A C1B C2B C3B C4B

[ mapping ]
charmm27 charmm36

[ atoms ]
1 N NC3
2 C12 NC3 NC3 NC3 PO4
3 C13 NC3
4 C14 NC3
5 C15 NC3
6 H12A NC3 NC3 NC3 PO4
7 H12B NC3 NC3 NC3 PO4
8 H13A NC3
9 H13B NC3
10 H13C NC3
11 H14A NC3
12 H14B NC3
13 H14C NC3
14 H15A NC3
15 H15B NC3
16 H15C NC3
17 C11 NC3 PO4
18 H11A NC3 PO4
19 H11B NC3 PO4
20 P PO4
21 O13 PO4
22 O14 PO4
23 O12 PO4 PO4 PO4 NC3
24 O11 PO4 PO4 GL1
25 C1 GL1 GL1 PO4
26 HA GL1 GL1 PO4
27 HB GL1 GL1 PO4
28 C2 GL1 GL1 GL2
29 HS GL1 GL1 GL2
30 O21 GL1 GL1 GL2 C1A
31 C21 GL1 C1A
32 O22 GL1
33 C22 C1A C1A GL1
34 H2R C1A C1A GL1
35 H2S C1A C1A GL1
36 C3 GL2 GL2 GL2 PO4
37 HX GL2 GL2 GL2 PO4
38 HY GL2 GL2 GL2 PO4
39 O31 GL2
40 C31 GL2 GL1 C1B
41 O32 GL2
42 C32 C1B C1B GL2
43 H2X C1B C1B GL2
44 H2Y C1B C1B GL2
; First tail
45 C23 C1A
46 H3R
47 H3S
48 C24 C1A C1A C1A D2A
49 H4R
50 H4S
51 C25 C1A D2A
52 H5R
53 H5S
54 C26 D2A D2A D2A C1A
55 H6R
56 H6S
57 C27 D2A
58 H7R
59 H7S
60 C28 D2A D2A D2A C3A
61 H8R
62 H8S
63 C29 D2A D2A C3A
64 H91 D2A C3A
65 C210 C3A C3A D2A
66 H101 D2A C3A
67 C211 C3A C3A C3A D2A
68 H11R
69 H11S
70 C212 C3A
71 H12R
72 H12S
73 C213 C3A C3A C3A C4A
74 H13R
75 H13S
76 C214 C3A C4A
77 H14R
78 H14S
79 C215 C4A C4A C4A C3A
80 H15R
81 H15S
82 C216 C4A
83 H16R
84 H16S
85 C217 C4A
86 H17R
87 H17S
88 C218 C4A
89 H18R
90 H18S
91 H18T
; Other tail
92 C33 C1B
93 H3X C1B
94 H3Y C1B
95 C34 C1B C1B C2B
96 H4X C1B C1B C2B
97 H4Y C1B C1B C2B
98 C35 C1B C2B
99 H5X C1B C2B
100 H5Y C1B C2B
101 C36 C2B C2B C1B
102 H6X C2B C2B C1B
103 H6Y C2B C2B C1B
104 C37 C2B
105 H7X C2B
106 H7Y C2B
107 C38 C2B C2B C2B C3B
108 H8X C2B C2B C2B C3B
109 H8Y C2B C2B C2B C3B
110 C39 C2B C2B C3B
111 H9X C2B C2B C3B
112 H9Y C2B C2B C3B
113 C310 C3B C2B
114 H10X C3B C2B
115 H10Y C3B C2B
116 C311 C3B C3B C2B
117 H11X C3B C3B C2B
118 H11Y C3B C3B C2B
119 C312 C3B
120 H12X C3B
121 H12Y C3B
122 C313 C3B C3B C4B
123 H13X C3B C3B C4B
124 H13Y C3B C3B C4B
125 C314 C4B C3B
126 H14X C4B C3B
127 H14Y C4B C3B
128 C315 C4B C4B C3B
129 H15X C4B C4B C3B
130 H15Y C4B C4B C3B
131 C316 C4B
132 H16X C4B
133 H16Y C4B
134 H16Z C4B

;making R stereoisomer- placing HS
[chiral]
HS C2 O21 C1 C3

; acyl esters
[trans]
C22 C21 O21 C2
[ out ]
O22 C21 O21 C22
[trans]
C32 C31 O31 C3
[out]
O32 C31 O31 C32

;cis bonds in lipind chains
[ out ]
H9R C29 C28 C210
[ trans ]
H10R C210 C29 C28
[ out ]
C211 C210 C29 H10R

;;;making a choline group
[out]
C14 N C13 C12
H14A N C13 C12
H14B N C13 C12
H14C N C13 C12

[ chiral ]
C15 N C12 C13 C14
H15A N C12 C13 C14
H15B N C12 C13 C14
H15C N C12 C13 C14

; extend the tails
[ trans ]
C217 C216 C215 C214
C17R C216 C215 C214
C17S C216 C215 C214
C218 C217 C216 C215
C18R C217 C216 C215
C18S C217 C216 C215
C18T C217 C216 C215

; Cheers,

; Tsjerk

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8 years 5 months ago - 8 years 5 months ago #5197 by Stéfane
Replied by Stéfane on topic Backmapping an α-linolen chain with only 4 beads
Great !!

Thanks tsjerk for your quick help. It worked

A bientôt

Stéfane
Last edit: 8 years 5 months ago by Stéfane.

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