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Conversion of CG carbohydrate into a AA model
- Stéfane
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8 years 5 months ago - 8 years 5 months ago #5217
by Stéfane
Conversion of CG carbohydrate into a AA model was created by Stéfane
Hello hello,
I pursue my exploration of the backmapping approach by converting some CG glycolipids (GL) into atomistic models (charmm36). Thanks to Tsjerk, heigi and others, I can successfully transform different models of PG and mono glycolipids CG atomistic ones. However, since I simulated a GL membrane I would like to be "sure" that my GL atomistic models will have the same conformation (with the OH group at the right place). I know that I can use the [ chiral ] keyword in the mapping file, but I don't know how to use it with carbohydrates. Do you have a example to share with me?
BTW, I have another question of the atomistic transformation for Digalactose-based lipids simulated in the van Eerden et al. BBA 2015 paper. In this work, the CG Digalactose headgroup is modeled with only three beads. What is the mapping used by the authors to covert these molecules into FG models, or better an AA ones
Thanks again for your help
Stéfane
I pursue my exploration of the backmapping approach by converting some CG glycolipids (GL) into atomistic models (charmm36). Thanks to Tsjerk, heigi and others, I can successfully transform different models of PG and mono glycolipids CG atomistic ones. However, since I simulated a GL membrane I would like to be "sure" that my GL atomistic models will have the same conformation (with the OH group at the right place). I know that I can use the [ chiral ] keyword in the mapping file, but I don't know how to use it with carbohydrates. Do you have a example to share with me?
BTW, I have another question of the atomistic transformation for Digalactose-based lipids simulated in the van Eerden et al. BBA 2015 paper. In this work, the CG Digalactose headgroup is modeled with only three beads. What is the mapping used by the authors to covert these molecules into FG models, or better an AA ones
Thanks again for your help
Stéfane
Last edit: 8 years 5 months ago by Stéfane.
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- tsjerk
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8 years 5 months ago #5220
by tsjerk
Replied by tsjerk on topic Conversion of CG carbohydrate into a AA model
Hi Stéfane,
I don't know about the mapping for the digalactose headgroup. As for the other part of the question, it may be useful to have a look at the mapping of glucose and that of trehalose. I only have them for GROMOS currently, but you can just add the hydrogens. Just remember that no two particles will ever be placed at the same position, so you can usually just reuse the recipe for placing a heavy atom to place the corresponding hydrogens.
[ molecule ]
GLUC
[ martini ]
B1 B2 B3
;
; B1
; /\
; / \
; B2--B3
;
;
; Glucose
; Beta-D-glucopyranoside
;
; C6 - O6 - H6
; |
; C5 - O5 - C1 - O1 - H1
; | |
; C4 - C3 - C2
; | | |
; O4 O3 O2
; | | |
; H4 H3 H2
;
[ mapping ]
gromos gromos43a1 gromos43a2 gromos45a3 gromos45a4 gromos53a5 gromos53a6 gromos54a7 alex
[ atoms ]
1 C1 B1 B2 B3 B2 B2 B2
2 O1 B2
3 H1
4 C5 B1 B2 B3 B1 B1 B1
5 O5 B1 B2
6 C2 B2 B3
7 O2
8 HO2
9 C3 B1 B2 B3 B3 B3 B3
10 O3 B3
11 HO3
12 C4 B1 B3
13 O4
14 HO4
15 C6 B1
16 O6
17 HO6
; Building the ring
[ out ]
O2 C2 C1 C3
H2 C2 C1 C3
O4 C4 C3 C5
H4 C4 C3 C5
[ trans ]
O6 C6 C5 O5
H6 C6 C5 O5
H1 O1 C1 C2
H3 O3 C3 C4
[ chiral ]
C1 O1 C2 O5
C3 O3 C4 C2
C5 O5 C4 C6
C2 O2 C1 C3
C4 O4 C3 C5
[ molecule ]
TRE
[ martini ]
B1 B2 B3 B4 B5 B6
;
; B1 B5
; \ \
; B2----B4
; / /
; B3 B6
;
[ mapping ]
gromos gromos43a1 gromos43a2 gromos45a3 gromos45a4 gromos53a5 gromos53a6 gromos54a7 alex
[ atoms ]
1 O41 B2
2 HO41
3 C41
4 C31 B3 B2
5 O31 B3
6 HO31
7 C21
8 O21
9 HO21
10 C61 B1
11 O61
12 HO61
13 C51 B1 B2
14 O51
15 C11 B2 B2 B2 B4
16 O11 B2 B4
17 C42
18 O42 B4
19 HO42
20 C32 B6 B4
21 O32 B6
22 HO32
23 C22
24 O22
25 HO22
26 C62 B5
27 O62
28 HO62
29 C52 B4 B5
30 O52
31 C12 B4 B4 B4 B2
; Building first ring
; Note we 'stored' the B2 position on O41
[ trans ]
C21 C11 C31 O41
O51 C11 C51 O41
[ out ]
C41 O41 O51 C21
O21 C21 C11 C31
HO21 C21 C11 C31
O41 C41 C51 C31
HO41 C41 C51 C31
[ trans ]
O61 C61 C51 C41
HO61 C61 C51 C41
[ chiral ]
C11 O11 C21 O51
C31 O31 C41 C21
C51 O51 C41 C61
C21 O21 C11 C31
C41 O41 C31 C51
; Building second ring
; Note we 'stored' the B4 position on O42
[ trans ]
C22 C12 C32 O42
O52 C12 C52 O42
[ out ]
C42 O42 O52 C22
O22 C22 C12 C32
HO22 C22 C12 C32
O42 C42 C52 C32
HO42 C42 C52 C32
[ trans ]
O62 C62 C52 C42
HO62 C62 C52 C42
[ chiral ]
C12 O11 C22 O52
C32 O32 C42 C22
C52 O52 C42 C62
C22 O22 C12 C32
C42 O42 C32 C52
Cheers,
Tsjerk
I don't know about the mapping for the digalactose headgroup. As for the other part of the question, it may be useful to have a look at the mapping of glucose and that of trehalose. I only have them for GROMOS currently, but you can just add the hydrogens. Just remember that no two particles will ever be placed at the same position, so you can usually just reuse the recipe for placing a heavy atom to place the corresponding hydrogens.
[ molecule ]
GLUC
[ martini ]
B1 B2 B3
;
; B1
; /\
; / \
; B2--B3
;
;
; Glucose
; Beta-D-glucopyranoside
;
; C6 - O6 - H6
; |
; C5 - O5 - C1 - O1 - H1
; | |
; C4 - C3 - C2
; | | |
; O4 O3 O2
; | | |
; H4 H3 H2
;
[ mapping ]
gromos gromos43a1 gromos43a2 gromos45a3 gromos45a4 gromos53a5 gromos53a6 gromos54a7 alex
[ atoms ]
1 C1 B1 B2 B3 B2 B2 B2
2 O1 B2
3 H1
4 C5 B1 B2 B3 B1 B1 B1
5 O5 B1 B2
6 C2 B2 B3
7 O2
8 HO2
9 C3 B1 B2 B3 B3 B3 B3
10 O3 B3
11 HO3
12 C4 B1 B3
13 O4
14 HO4
15 C6 B1
16 O6
17 HO6
; Building the ring
[ out ]
O2 C2 C1 C3
H2 C2 C1 C3
O4 C4 C3 C5
H4 C4 C3 C5
[ trans ]
O6 C6 C5 O5
H6 C6 C5 O5
H1 O1 C1 C2
H3 O3 C3 C4
[ chiral ]
C1 O1 C2 O5
C3 O3 C4 C2
C5 O5 C4 C6
C2 O2 C1 C3
C4 O4 C3 C5
[ molecule ]
TRE
[ martini ]
B1 B2 B3 B4 B5 B6
;
; B1 B5
; \ \
; B2----B4
; / /
; B3 B6
;
[ mapping ]
gromos gromos43a1 gromos43a2 gromos45a3 gromos45a4 gromos53a5 gromos53a6 gromos54a7 alex
[ atoms ]
1 O41 B2
2 HO41
3 C41
4 C31 B3 B2
5 O31 B3
6 HO31
7 C21
8 O21
9 HO21
10 C61 B1
11 O61
12 HO61
13 C51 B1 B2
14 O51
15 C11 B2 B2 B2 B4
16 O11 B2 B4
17 C42
18 O42 B4
19 HO42
20 C32 B6 B4
21 O32 B6
22 HO32
23 C22
24 O22
25 HO22
26 C62 B5
27 O62
28 HO62
29 C52 B4 B5
30 O52
31 C12 B4 B4 B4 B2
; Building first ring
; Note we 'stored' the B2 position on O41
[ trans ]
C21 C11 C31 O41
O51 C11 C51 O41
[ out ]
C41 O41 O51 C21
O21 C21 C11 C31
HO21 C21 C11 C31
O41 C41 C51 C31
HO41 C41 C51 C31
[ trans ]
O61 C61 C51 C41
HO61 C61 C51 C41
[ chiral ]
C11 O11 C21 O51
C31 O31 C41 C21
C51 O51 C41 C61
C21 O21 C11 C31
C41 O41 C31 C51
; Building second ring
; Note we 'stored' the B4 position on O42
[ trans ]
C22 C12 C32 O42
O52 C12 C52 O42
[ out ]
C42 O42 O52 C22
O22 C22 C12 C32
HO22 C22 C12 C32
O42 C42 C52 C32
HO42 C42 C52 C32
[ trans ]
O62 C62 C52 C42
HO62 C62 C52 C42
[ chiral ]
C12 O11 C22 O52
C32 O32 C42 C22
C52 O52 C42 C62
C22 O22 C12 C32
C42 O42 C32 C52
Cheers,
Tsjerk
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8 years 5 months ago - 8 years 5 months ago #5221
by Stéfane
Replied by Stéfane on topic Conversion of CG carbohydrate into a AA model
Hi Tsjerk,
Thank you very much for your kind and quick reply. I will test these mappings. For the CG -> AA transformation of digalactose with three beads, I will contact the corresponding author of the paper to ask how they did.
Stéfane
Thank you very much for your kind and quick reply. I will test these mappings. For the CG -> AA transformation of digalactose with three beads, I will contact the corresponding author of the paper to ask how they did.
Stéfane
Last edit: 8 years 5 months ago by Stéfane.
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8 years 5 months ago #5222
by tsjerk
Replied by tsjerk on topic Conversion of CG carbohydrate into a AA model
Hi Stéfane,
Can you share the mappings if you have them? If you send a CG structure and atomistic topology along I can also validate the mapping for you.
Cheers,
Tsjerk
Can you share the mappings if you have them? If you send a CG structure and atomistic topology along I can also validate the mapping for you.
Cheers,
Tsjerk
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8 years 5 months ago - 8 years 5 months ago #5223
by Stéfane
Replied by Stéfane on topic Conversion of CG carbohydrate into a AA model
No problem
Cheers
Stéfane
Cheers
Stéfane
Last edit: 8 years 5 months ago by Stéfane. Reason: Modification of the initial message
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8 years 5 months ago - 8 years 5 months ago #5230
by Stéfane
Replied by Stéfane on topic Conversion of CG carbohydrate into a AA model
Tsjerk,
I have tested your mapping scheme for glucose in my model of monogalactoselipids (MDG) (with, of course, some changes to have the correct sugar) to obtain AA models compatibles with the CHARMM36. It works fine for one molecule but not for all the MDG in my membrane. Indeed sometimes the OH and CH2OH in sugar ring are well oriented sometimes not. How to avoid this problem?
Cheers
Stéfane
I have tested your mapping scheme for glucose in my model of monogalactoselipids (MDG) (with, of course, some changes to have the correct sugar) to obtain AA models compatibles with the CHARMM36. It works fine for one molecule but not for all the MDG in my membrane. Indeed sometimes the OH and CH2OH in sugar ring are well oriented sometimes not. How to avoid this problem?
Cheers
Stéfane
Last edit: 8 years 5 months ago by Stéfane.
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