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MARTINI BACKMAPPING
- shakira
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2 years 4 months ago #9248
by shakira
MARTINI BACKMAPPING was created by shakira
Hi
I am trying to backmap a raft structure of DPPC/DUPC/CHOL mixture of 1:1:0.8 composition after a 40 microsecond MARTINI simulation. I have used the DPPC and CHOL charmm36.map files and since DUPC map file is not available for download i wrote it myself looking into DPPC and DOPC map files. My system after backmapping has around 2.25 million particles including backmapped water molecules. I observed that only the first step (steep minimisation excluding non bonded interactions) run went well and the succeeding steps throw LINCS warning with huge PE. I tried to run it seprately from the output gro file of first step energy minimization. But that was not of any help. I could not fix the issue and did not find any useful links discussed on this anywhere in the MARTINI FORUM. I am wondering does the error comes from the huge size of my system or the map file of DUPC lipid. I am copying the map file for DUPC here for reference.
; Mapping file created 28/02/2013 by Kri
[ molecule ]
DUPC
[ martini ]
NC3 PO4 GL1 GL2 C1A D2A D3A C4A C1B D2B D3B C4B
;
; NC3-PO4-GL1-C1A-D2A-D3A-C4A
; |
; GL2-C1B-D2B-D3B-C4B
[ mapping ]
charmm36
[ atoms ]
; Terminal head group (choline)
1 N NC3
2 C12 NC3 NC3 NC3 PO4
3 H12A NC3 NC3 NC3 PO4
4 H12B NC3 NC3 NC3 PO4
5 C13 NC3
6 H13A NC3
7 H13B NC3
8 H13C NC3
9 C14 NC3
10 H14A NC3
11 H14B NC3
12 H14C NC3
13 C15 NC3
14 H15A NC3
15 H15B NC3
16 H15C NC3
17 C11 NC3 PO4
18 H11A NC3 PO4
19 H11B NC3 PO4
; Phosphate group
20 P PO4
21 O13 PO4
22 O14 PO4
23 O12 PO4 PO4 PO4 NC3
24 O11 PO4 PO4 GL1
; Diacylglycerol
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
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 D3A
61 H8R
62 H8S
63 C29 D2A D2A D3A
64 H9R D2A D3A
65 C210 D3A D3A D2A
66 H10R D2A D3A
67 C211 D3A D3A D3A D2A
68 H11R
69 H11S
70 C212 D3A
71 H12R D3A
72 C213 D3A D3A D3A C4A
73 H13R D3A C4A
74 C214 D3A C4A
75 H14R
76 H14S
77 C215 C4A C4A C4A D3A
78 H15R
79 H15S
80 C216 C4A
81 H16R
82 H16S
83 C217 C4A
84 H17R
85 H17S
86 C218 C4A
87 H18R
88 H18S
89 H18T
90 C33 C1B
91 H3X
92 H3Y
93 C34 C1B C1B C1B D2B
94 H4X
95 H4Y
96 C35 C1B D2B
97 H5X
98 H5Y
99 C36 D2B D2B D2B C1B
100 H6X
101 H6Y
102 C37 D2B
103 H7X
104 H7Y
105 C38 D2B D2B D2B D3B
106 H8X
107 H8Y
108 C39 D2B D2B D3B
109 H9X D2B D3A
110 C310 D3B D3B D2B
111 H10X D2B D3B
112 C311 D3B D3B D3B D2B
113 H11X
114 H11Y
115 C312 D3B
116 H12X
117 C313 D3B D3B D3B C4B
118 H13X
119 C314 D3B C4B
120 H14X
121 H14Y
122 C315 C4B C4B C4B D3B
123 H15X
124 H15Y
125 C316 C4B
126 H16X
127 H16Y
128 C317 C4B
129 H17X
130 H17Y
131 C318 C4B
132 H18X
133 H18Y
134 H18Z
;;;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
;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 ]
H7R C27 C26 C28
H7S C27 C26 C28
C28 C27 C26 H7R
[ trans ]
C29 C28 C27 C26
C210 C29 C28 C27
H10R C210 C29 C28
[ out ]
C211 C210 H10R C29
H9R C29 C210 C28
[ out ]
H7X C37 C36 C38
H7Y C37 C36 C38
C38 C37 C36 H7X
[ trans ]
C39 C38 C37 C36
C310 C39 C38 C37
H10X C310 C39 C38
[ out ]
C311 C310 H10X C39
H9X C39 C310 C38
[ out ]
H15R C215 C216 C214
H15S C215 C216 C214
C214 C215 C216 H15R
[ trans ]
C213 C214 C215 C216
C212 C213 C214 C215
[ out ]
C211 C212 H12R C213
H13R C213 C212 C214
[ out ]
H15R C315 C316 C314
H15S C315 C316 C314
C314 C315 C316 H15R
[ trans ]
C313 C314 C315 C316
C312 C313 C314 C315
[ out ]
C311 C312 H12R C313
H13R C313 C312 C314
Any suggestions will be highly appreciated. Thanks in advance.
I am trying to backmap a raft structure of DPPC/DUPC/CHOL mixture of 1:1:0.8 composition after a 40 microsecond MARTINI simulation. I have used the DPPC and CHOL charmm36.map files and since DUPC map file is not available for download i wrote it myself looking into DPPC and DOPC map files. My system after backmapping has around 2.25 million particles including backmapped water molecules. I observed that only the first step (steep minimisation excluding non bonded interactions) run went well and the succeeding steps throw LINCS warning with huge PE. I tried to run it seprately from the output gro file of first step energy minimization. But that was not of any help. I could not fix the issue and did not find any useful links discussed on this anywhere in the MARTINI FORUM. I am wondering does the error comes from the huge size of my system or the map file of DUPC lipid. I am copying the map file for DUPC here for reference.
; Mapping file created 28/02/2013 by Kri
[ molecule ]
DUPC
[ martini ]
NC3 PO4 GL1 GL2 C1A D2A D3A C4A C1B D2B D3B C4B
;
; NC3-PO4-GL1-C1A-D2A-D3A-C4A
; |
; GL2-C1B-D2B-D3B-C4B
[ mapping ]
charmm36
[ atoms ]
; Terminal head group (choline)
1 N NC3
2 C12 NC3 NC3 NC3 PO4
3 H12A NC3 NC3 NC3 PO4
4 H12B NC3 NC3 NC3 PO4
5 C13 NC3
6 H13A NC3
7 H13B NC3
8 H13C NC3
9 C14 NC3
10 H14A NC3
11 H14B NC3
12 H14C NC3
13 C15 NC3
14 H15A NC3
15 H15B NC3
16 H15C NC3
17 C11 NC3 PO4
18 H11A NC3 PO4
19 H11B NC3 PO4
; Phosphate group
20 P PO4
21 O13 PO4
22 O14 PO4
23 O12 PO4 PO4 PO4 NC3
24 O11 PO4 PO4 GL1
; Diacylglycerol
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
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 D3A
61 H8R
62 H8S
63 C29 D2A D2A D3A
64 H9R D2A D3A
65 C210 D3A D3A D2A
66 H10R D2A D3A
67 C211 D3A D3A D3A D2A
68 H11R
69 H11S
70 C212 D3A
71 H12R D3A
72 C213 D3A D3A D3A C4A
73 H13R D3A C4A
74 C214 D3A C4A
75 H14R
76 H14S
77 C215 C4A C4A C4A D3A
78 H15R
79 H15S
80 C216 C4A
81 H16R
82 H16S
83 C217 C4A
84 H17R
85 H17S
86 C218 C4A
87 H18R
88 H18S
89 H18T
90 C33 C1B
91 H3X
92 H3Y
93 C34 C1B C1B C1B D2B
94 H4X
95 H4Y
96 C35 C1B D2B
97 H5X
98 H5Y
99 C36 D2B D2B D2B C1B
100 H6X
101 H6Y
102 C37 D2B
103 H7X
104 H7Y
105 C38 D2B D2B D2B D3B
106 H8X
107 H8Y
108 C39 D2B D2B D3B
109 H9X D2B D3A
110 C310 D3B D3B D2B
111 H10X D2B D3B
112 C311 D3B D3B D3B D2B
113 H11X
114 H11Y
115 C312 D3B
116 H12X
117 C313 D3B D3B D3B C4B
118 H13X
119 C314 D3B C4B
120 H14X
121 H14Y
122 C315 C4B C4B C4B D3B
123 H15X
124 H15Y
125 C316 C4B
126 H16X
127 H16Y
128 C317 C4B
129 H17X
130 H17Y
131 C318 C4B
132 H18X
133 H18Y
134 H18Z
;;;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
;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 ]
H7R C27 C26 C28
H7S C27 C26 C28
C28 C27 C26 H7R
[ trans ]
C29 C28 C27 C26
C210 C29 C28 C27
H10R C210 C29 C28
[ out ]
C211 C210 H10R C29
H9R C29 C210 C28
[ out ]
H7X C37 C36 C38
H7Y C37 C36 C38
C38 C37 C36 H7X
[ trans ]
C39 C38 C37 C36
C310 C39 C38 C37
H10X C310 C39 C38
[ out ]
C311 C310 H10X C39
H9X C39 C310 C38
[ out ]
H15R C215 C216 C214
H15S C215 C216 C214
C214 C215 C216 H15R
[ trans ]
C213 C214 C215 C216
C212 C213 C214 C215
[ out ]
C211 C212 H12R C213
H13R C213 C212 C214
[ out ]
H15R C315 C316 C314
H15S C315 C316 C314
C314 C315 C316 H15R
[ trans ]
C313 C314 C315 C316
C312 C313 C314 C315
[ out ]
C311 C312 H12R C313
H13R C313 C312 C314
Any suggestions will be highly appreciated. Thanks in advance.
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- Posts: 21
2 years 4 months ago #9266
by shakira
Replied by shakira on topic MARTINI BACKMAPPING
Hi
any suggestion will be greatly helpful for me. Where am I going wrong? Is it the mapping file for DUPC which we have written ourselves with reference to DPPC and DOPC or is it system size that causes issues?
any suggestion will be greatly helpful for me. Where am I going wrong? Is it the mapping file for DUPC which we have written ourselves with reference to DPPC and DOPC or is it system size that causes issues?
Please Log in or Create an account to join the conversation.
- shakira
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Topic Author
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- Posts: 21
2 years 4 months ago #9267
by shakira
Replied by shakira on topic MARTINI BACKMAPPING
Hi
I understood its the problem with the DUPC mapping file that I have written. When I ran a smaller DUPC martini system and tried to backmap it shows me the same LINCS warning errors. Where can I get the mapping file for DUPC martini system.
Thanks in advance
I understood its the problem with the DUPC mapping file that I have written. When I ran a smaller DUPC martini system and tried to backmap it shows me the same LINCS warning errors. Where can I get the mapping file for DUPC martini system.
Thanks in advance
Please Log in or Create an account to join the conversation.
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