normal backward with POPE and POPS

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5 years 2 months ago - 5 years 2 months ago #7999 by soltak
backward with POPE and POPS was created by soltak
I am trying to backward a POPE/POPS lipid bilayer to charmm36, but couldn't find the mapping files. Could anyone provide me the mapping files? Thanks!

Yong Wang
Postdoc in Lindorff-Larsen Lab
Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science
Department of Biology, University of Copenhagen
Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
Last edit: 5 years 2 months ago by soltak. Reason: typos

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5 years 2 months ago #8007 by bart
Replied by bart on topic backward with POPE and POPS
To my understanding only some example backward files were provided. In the backward paper and this tutorial , you can find how to create your own mapping files.

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5 years 2 months ago - 5 years 2 months ago #8008 by riccardo
Replied by riccardo on topic backward with POPE and POPS
Indeed. Make sure to also check the lipidome ( cgmartini.nl/index.php/force-field-parameters/lipids ). Some mapping files may be there but not in the backward "Mapping" directory. I quickly checked for POPE and POPS and found indeed no mapping files, e.g., see POPE at cgmartini.nl/index.php/force-field-param...ml?dir=PE&lipid=POPE
Last edit: 5 years 2 months ago by riccardo.

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5 years 2 months ago #8009 by soltak
Replied by soltak on topic backward with POPE and POPS
Thanks a lot for your reply, both Riccardo and Bart.

Yeah, I do find some mapping files, e.g. for POPC, but not for POPE and POPS. Alright, I will follow the tutorial and make my own mapping files. Thanks!

Yong

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5 years 2 months ago #8010 by tsjerk
Replied by tsjerk on topic backward with POPE and POPS
Have you checked the repository on Github ( www.github.com/Tsjerk/Backward )? The mappings for these lipids should are already available.

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5 years 2 months ago #8011 by soltak
Replied by soltak on topic backward with POPE and POPS
Woo! Fantastic. Sorry, I didn't check the github version. I thought it is the same version as the one from the cgmartini website. Yes, the mapping files for both POPE and POPS are there. Thank you so much, Tsjerk!
Issue closed!

Yong

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5 years 1 month ago #8028 by bart
Replied by bart on topic backward with POPE and POPS
I did not know about the mapping files available on github and I will see if we can merge these databases or at least link to it in a clear manner.

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4 years 2 weeks ago #8468 by hsharma
Replied by hsharma on topic backward with POPE and POPS
It turns out that the POPS beads have mismatched bead definition in the .gro file
( www.cgmartini.nl/images/parameters/lipids/PS/POPS/POPS-em.gro ) and in the mapping file defined in backmapping.( github.com/Tsjerk/Backward/blob/master/M...ng/pops.charmm36.map ).

Coordinate definition has 4 beads on B tail however has 5 beads on B tail in mapping file.

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4 years 2 weeks ago #8469 by tsjerk
Replied by tsjerk on topic backward with POPE and POPS
Ah, the old-style lipids, still. You should be able to solve it by putting the following section before the [ atoms ] section in the mapping file:

[ assign ]
; Mapping from old style (5-bead) tail to new style (4-bead)
D2A C2A C2A D3A
C3A C4A C4A D3A
C4A C5A


If that solves the problem, please let me know; I'll push the change to GitHub for all PO lipids then. Otherwise, I'll have to put some more effort in ;)

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4 years 2 weeks ago - 4 years 2 weeks ago #8470 by hsharma
Replied by hsharma on topic backward with POPE and POPS
With the new suggestion: my first few lines of pops.charmm36.map file looks like,

[ molecule ]
POPS

[ martini ]
CNO PO4 GL1 GL2 C1A C2A C3A C4A C1B C2B D3B C4B C5B

[ mapping ]
charmm27 charmm36

[ assign ]
; Mapping from old style (5-bead) tail to new style (4-bead)

D2A C2A C2A D3A
C3A C4A C4A D3A
C4A C5A


[ atoms ]
1 N CNO
2 HN1 CNO
3 HN2 CNO
4 HN3 CNO
However it did not worked.

Since the new pope.charmm36.map is most similar to the required pops.charmm36.map according to the new bead definition of pops martini lipid, I made it to work by replacing some beads in pope.charmm36.map by the ones from pops. i.e, replacing NH3 in pope.charmm36.map to CNO. This will be the one we require.

Hari
Last edit: 4 years 2 weeks ago by hsharma. Reason: typo

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2 years 7 months ago #9083 by cneale
Replied by cneale on topic backward with POPE and POPS
For posterity, Tsjerk's [ assign ] solution does not work because the old and new versions swap the "A" and "B" definitions of the tails. In the old style, GL1 is connected to C1B, but in the new style GL1 is connected to C1A. At least I think this is the case.

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2 years 7 months ago #9084 by cneale
Replied by cneale on topic backward with POPE and POPS
Here's a version of POPS mapping I put together by taking the 12-bead POPC map file, replacing the choline head group atoms and directives sections with those from the 13-bead POPS map file. Seems to work OK.

; latest revision TAW 20160213 -- was POPC, then CN modified to POPS
[ molecule ]
POPS

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

[ mapping ]
charmm27 charmm36 slipids amber

[ atoms ]
1 N CNO
2 HN1 CNO
3 HN2 CNO
4 HN3 CNO
5 C12 CNO CNO CNO PO4
6 H12A CNO CNO CNO PO4
7 C13 CNO
8 O13A CNO
9 O13B CNO
10 C11 PO4 CNO
11 H11A PO4 CNO
12 H11B PO4 CNO
20 P PO4
21 O13 PO4
22 O14 PO4
23 O12 PO4 PO4 PO4 CNO
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
[out]
C13 N C3 C11
[chiral]
H12A C12 N C11 C13
[chiral]
C13 C12 H12A C11 N
O13A C12 H12A C11 N
O13B C12 H12A C11 N


;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 lipid chains
;[ out ]
;H91 C29 C28 C210
;C210 C29 H91 C28
;C28 C29 H91 C210
;[ trans ]
;C211 C210 C29 H91
;H101 C210 C29 C28
;H91 C29 C210 C211
;C28 C29 C210 H101
[ out ]
H7R C27 C26 C28
H7S C27 C26 C28
C28 C27 C26 H7R
H8R C27 C26 H7R
H8S C27 C26 H7R

[ trans ]
C29 C28 C27 C26
C210 C29 C28 C27
H101 C210 C29 C28
[ out ]
C211 C210 H101 C29
H11R C210 H101 C29
H11S C210 H101 C29
H91 C29 C210 C28

; extend the tails
[ trans ]
C217 C216 C215 C214
H17R C216 C215 C214
H17S C216 C215 C214
C218 C217 C216 C215
H18R C217 C216 C215
H18S C217 C216 C215
H18T C217 C216 C215

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