normal Oleic acid backmap

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3 years 2 months ago #8811 by bellafrizzo
Oleic acid backmap was created by bellafrizzo
Hello there,

I wish I retrieved map file for this oleic acid topology

[moleculetype]
; molname nrexcl
OLAC 2

[atoms]
; id type resnr residue atom cgnr charge mass typeB chargeB massB smiles
1 C3 1 OLAC C01 1 0 72.0 ; CCC
2 C3 1 OLAC C02 2 0 72.0 ; CCC
3 C1 1 OLAC C03 3 0 72.0 ; CCC=CC
4 C3 1 OLAC C04 4 0 72.0 ; CCC
5 C5 1 OLAC C05 5 0 72.0 ; CC
6 P1 1 OLAC P01 6 0 72.0 Qa -1 72.0 ; CC(O)=O

[bonds]
; i j funct length force.c.
1 2 1 0.25 1250
2 3 1 0.34 1250
3 4 1 0.37 1250
4 5 1 0.32 1250
5 6 1 0.25 1250

[angles]
; i j k funct angle force.c.
1 2 3 2 133.0 25.0
2 3 4 2 68.7 45.0
3 4 5 2 97.9 25.0
4 5 6 2 88.6 25.0

How can I backmap to full atom resolution as in

[ moleculetype ]
; Name nrexcl
HA2N 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 HS14 1 HA2N H34 1 0.242 1.0080
2 OA 1 HA2N O2 2 -0.319 15.9994
3 CPos 1 HA2N C1 3 0.302 12.0110
4 OEOpt 1 HA2N O1 4 -0.361 15.9994
5 C 1 HA2N C2 5 -0.154 12.0110
6 HC 1 HA2N H1 6 0.118 1.0080
7 HC 1 HA2N H2 7 0.118 1.0080
8 C 1 HA2N C3 8 -0.156 12.0110
9 HC 1 HA2N H3 9 0.095 1.0080
10 HC 1 HA2N H4 10 0.095 1.0080
11 C 1 HA2N C4 11 -0.158 12.0110
12 HC 1 HA2N H5 12 0.082 1.0080
13 HC 1 HA2N H6 13 0.082 1.0080
14 C 1 HA2N C5 14 -0.158 12.0110
15 HC 1 HA2N H7 15 0.082 1.0080
16 HC 1 HA2N H8 16 0.082 1.0080
17 C 1 HA2N C6 17 -0.158 12.0110
18 HC 1 HA2N H9 18 0.080 1.0080
19 HC 1 HA2N H10 19 0.080 1.0080
20 C 1 HA2N C7 20 -0.156 12.0110
21 HC 1 HA2N H11 21 0.082 1.0080
22 HC 1 HA2N H12 22 0.082 1.0080
23 C 1 HA2N C8 23 -0.132 12.0110
24 HC 1 HA2N H13 24 0.087 1.0080
25 HC 1 HA2N H14 25 0.087 1.0080
26 C 1 HA2N C9 26 -0.171 12.0110
27 HC 1 HA2N H15 27 0.122 1.0080
28 C 1 HA2N C10 28 -0.168 12.0110
29 HC 1 HA2N H16 29 0.122 1.0080
30 C 1 HA2N C11 30 -0.132 12.0110
31 HC 1 HA2N H17 31 0.087 1.0080
32 HC 1 HA2N H18 32 0.087 1.0080
33 C 1 HA2N C12 33 -0.156 12.0110
34 HC 1 HA2N H19 34 0.081 1.0080
35 HC 1 HA2N H20 35 0.081 1.0080
36 C 1 HA2N C13 36 -0.158 12.0110
37 HC 1 HA2N H21 37 0.079 1.0080
38 HC 1 HA2N H22 38 0.079 1.0080
39 C 1 HA2N C14 39 -0.158 12.0110
40 HC 1 HA2N H23 40 0.079 1.0080
41 HC 1 HA2N H24 41 0.079 1.0080
42 C 1 HA2N C15 42 -0.158 12.0110
43 HC 1 HA2N H25 43 0.079 1.0080
44 HC 1 HA2N H26 44 0.079 1.0080
45 C 1 HA2N C16 45 -0.158 12.0110
46 HC 1 HA2N H27 46 0.079 1.0080
47 HC 1 HA2N H28 47 0.079 1.0080
48 C 1 HA2N C17 48 -0.159 12.0110
49 HC 1 HA2N H29 49 0.078 1.0080
50 HC 1 HA2N H30 50 0.078 1.0080
51 C 1 HA2N C18 51 -0.210 12.0110
52 HC 1 HA2N H31 52 0.072 1.0080
53 HC 1 HA2N H32 53 0.072 1.0080
54 HC 1 HA2N H33 54 0.072 1.0080
; total charge of the molecule: 0.000
[ bonds ]
; ai aj funct c0 c1
1 2 2 0.0971 7.9547e+06
2 3 2 0.1360 1.0200e+07
3 4 2 0.1230 1.6600e+07
3 5 2 0.1500 8.3700e+06
5 6 2 0.1120 3.7000e+07
5 7 2 0.1120 3.7000e+07
5 8 2 0.1520 5.4300e+06
8 9 2 0.1120 3.7000e+07
8 10 2 0.1120 3.7000e+07
8 11 2 0.1520 5.4300e+06
11 12 2 0.1120 3.7000e+07
11 13 2 0.1120 3.7000e+07
11 14 2 0.1520 5.4300e+06
14 15 2 0.1120 3.7000e+07
14 16 2 0.1120 3.7000e+07
14 17 2 0.1520 5.4300e+06
17 18 2 0.1120 3.7000e+07
17 19 2 0.1120 3.7000e+07
17 20 2 0.1520 5.4300e+06
20 21 2 0.1120 3.7000e+07
20 22 2 0.1120 3.7000e+07
20 23 2 0.1520 5.4300e+06
23 24 2 0.1130 7.0483e+06
23 25 2 0.1130 7.0483e+06
23 26 2 0.1480 5.7300e+06
26 27 2 0.1100 1.2100e+07
26 28 2 0.1330 1.1800e+07
28 29 2 0.1100 1.2100e+07
28 30 2 0.1480 5.7300e+06
30 31 2 0.1130 7.0483e+06
30 32 2 0.1130 7.0483e+06
30 33 2 0.1520 5.4300e+06
33 34 2 0.1120 3.7000e+07
33 35 2 0.1120 3.7000e+07
33 36 2 0.1520 5.4300e+06
36 37 2 0.1120 3.7000e+07
36 38 2 0.1120 3.7000e+07
36 39 2 0.1520 5.4300e+06
39 40 2 0.1120 3.7000e+07
39 41 2 0.1120 3.7000e+07
39 42 2 0.1520 5.4300e+06
42 43 2 0.1120 3.7000e+07
42 44 2 0.1120 3.7000e+07
42 45 2 0.1520 5.4300e+06
45 46 2 0.1120 3.7000e+07
45 47 2 0.1120 3.7000e+07
45 48 2 0.1520 5.4300e+06
48 49 2 0.1120 3.7000e+07
48 50 2 0.1120 3.7000e+07
48 51 2 0.1510 3.7279e+06
51 52 2 0.1120 3.7000e+07
51 53 2 0.1120 3.7000e+07
51 54 2 0.1120 3.7000e+07
[ pairs ]
; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp
1 4 1
1 5 1
2 6 1
2 7 1
2 8 1
3 9 1
3 10 1
3 11 1
4 6 1
4 7 1
4 8 1
5 12 1
5 13 1
5 14 1
6 9 1
6 10 1
6 11 1
7 9 1
7 10 1
7 11 1
8 15 1
8 16 1
8 17 1
9 12 1
9 13 1
9 14 1
10 12 1
10 13 1
10 14 1
11 18 1
11 19 1
11 20 1
12 15 1
12 16 1
12 17 1
13 15 1
13 16 1
13 17 1
14 21 1
14 22 1
14 23 1
15 18 1
15 19 1
15 20 1
16 18 1
16 19 1
16 20 1
17 24 1
17 25 1
17 26 1
18 21 1
18 22 1
18 23 1
19 21 1
19 22 1
19 23 1
20 27 1
20 28 1
21 24 1
21 25 1
21 26 1
22 24 1
22 25 1
22 26 1
23 29 1
23 30 1
24 27 1
24 28 1
25 27 1
25 28 1
26 31 1
26 32 1
26 33 1
27 29 1
27 30 1
28 34 1
28 35 1
28 36 1
29 31 1
29 32 1
29 33 1
30 37 1
30 38 1
30 39 1
31 34 1
31 35 1
31 36 1
32 34 1
32 35 1
32 36 1
33 40 1
33 41 1
33 42 1
34 37 1
34 38 1
34 39 1
35 37 1
35 38 1
35 39 1
36 43 1
36 44 1
36 45 1
37 40 1
37 41 1
37 42 1
38 40 1
38 41 1
38 42 1
39 46 1
39 47 1
39 48 1
40 43 1
40 44 1
40 45 1
41 43 1
41 44 1
41 45 1
42 49 1
42 50 1
42 51 1
43 46 1
43 47 1
43 48 1
44 46 1
44 47 1
44 48 1
45 52 1
45 53 1
45 54 1
46 49 1
46 50 1
46 51 1
47 49 1
47 50 1
47 51 1
49 52 1
49 53 1
49 54 1
50 52 1
50 53 1
50 54 1
[ angles ]
; ai aj ak funct angle fc
1 2 3 2 109.50 450.00
2 3 4 2 117.00 635.00
2 3 5 2 115.00 610.00
4 3 5 2 126.00 640.00
3 5 6 2 109.00 1680.51
3 5 7 2 109.00 1680.51
3 5 8 2 111.00 530.00
6 5 7 2 108.53 443.00
6 5 8 2 110.00 285.00
7 5 8 2 110.00 285.00
5 8 9 2 109.60 450.00
5 8 10 2 109.60 450.00
5 8 11 2 111.00 530.00
9 8 10 2 107.57 484.00
9 8 11 2 109.60 450.00
10 8 11 2 109.60 450.00
8 11 12 2 109.60 450.00
8 11 13 2 109.60 450.00
8 11 14 2 111.00 530.00
12 11 13 2 107.00 2726.16
12 11 14 2 109.60 450.00
13 11 14 2 109.60 450.00
11 14 15 2 109.60 450.00
11 14 16 2 109.60 450.00
11 14 17 2 111.00 530.00
15 14 16 2 107.00 2726.16
15 14 17 2 109.60 450.00
16 14 17 2 109.60 450.00
14 17 18 2 109.60 450.00
14 17 19 2 109.60 450.00
14 17 20 2 111.00 530.00
18 17 19 2 107.00 2726.16
18 17 20 2 109.60 450.00
19 17 20 2 109.60 450.00
17 20 21 2 109.60 450.00
17 20 22 2 109.60 450.00
17 20 23 2 111.00 530.00
21 20 22 2 107.00 2726.16
21 20 23 2 109.60 450.00
22 20 23 2 109.60 450.00
20 23 24 2 109.50 285.00
20 23 25 2 109.50 285.00
20 23 26 2 111.00 530.00
24 23 25 2 106.75 503.00
24 23 26 2 109.60 450.00
25 23 26 2 109.60 450.00
23 26 27 2 120.00 505.00
23 26 28 2 126.00 640.00
27 26 28 2 120.00 505.00
26 28 29 2 120.00 505.00
26 28 30 2 126.00 640.00
29 28 30 2 120.00 505.00
28 30 31 2 109.60 450.00
28 30 32 2 109.60 450.00
28 30 33 2 111.00 530.00
31 30 32 2 106.75 503.00
31 30 33 2 109.50 285.00
32 30 33 2 109.50 285.00
30 33 34 2 109.60 450.00
30 33 35 2 109.60 450.00
30 33 36 2 111.00 530.00
34 33 35 2 107.00 2726.16
34 33 36 2 109.60 450.00
35 33 36 2 109.60 450.00
33 36 37 2 109.60 450.00
33 36 38 2 109.60 450.00
33 36 39 2 111.00 530.00
37 36 38 2 107.00 2726.16
37 36 39 2 109.60 450.00
38 36 39 2 109.60 450.00
36 39 40 2 109.60 450.00
36 39 41 2 109.60 450.00
36 39 42 2 111.00 530.00
40 39 41 2 107.00 2726.16
40 39 42 2 109.60 450.00
41 39 42 2 109.60 450.00
39 42 43 2 109.60 450.00
39 42 44 2 109.60 450.00
39 42 45 2 111.00 530.00
43 42 44 2 107.00 2726.16
43 42 45 2 109.60 450.00
44 42 45 2 109.60 450.00
42 45 46 2 109.60 450.00
42 45 47 2 109.60 450.00
42 45 48 2 111.00 530.00
46 45 47 2 107.00 2726.16
46 45 48 2 109.50 285.00
47 45 48 2 109.50 285.00
45 48 49 2 109.50 285.00
45 48 50 2 109.50 285.00
45 48 51 2 111.00 530.00
49 48 50 2 107.00 2726.16
49 48 51 2 109.60 450.00
50 48 51 2 109.60 450.00
48 51 52 2 110.30 524.00
48 51 53 2 110.30 524.00
48 51 54 2 110.30 524.00
52 51 53 2 108.53 443.00
52 51 54 2 108.53 443.00
53 51 54 2 108.53 443.00
[ dihedrals ]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
3 2 4 5 2 0.00 167.36
26 23 27 28 2 0.00 167.36
28 26 29 30 2 0.00 167.36
[ dihedrals ]
; ai aj ak al funct ph0 cp mult
1 2 3 5 1 180.00 16.70 2
3 5 8 11 1 0.00 5.92 3
4 3 5 8 1 0.00 1.00 6
5 8 11 14 1 0.00 5.92 3
8 11 14 17 1 0.00 5.92 3
11 14 17 20 1 0.00 5.92 3
14 17 20 23 1 0.00 5.92 3
17 20 23 26 1 0.00 5.92 3
20 23 26 28 1 180.00 1.00 6
23 26 28 30 1 180.00 41.80 2
26 28 30 33 1 180.00 1.00 6
28 30 33 36 1 0.00 5.92 3
30 33 36 39 1 0.00 5.92 3
33 36 39 42 1 0.00 5.92 3
36 39 42 45 1 0.00 5.92 3
39 42 45 48 1 0.00 5.92 3
42 45 48 51 1 0.00 5.92 3
45 48 51 52 1 0.00 5.92 3
[ exclusions ]
; ai aj funct ; GROMOS 1-4 exclusions

Thank you in advance for your input
Matteo

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3 years 1 month ago #8815 by riccardo
Replied by riccardo on topic Oleic acid backmap
If you can't find a mapping with backward's default mappings (which I think are mostly amino acids) and the Martini lipidome (lipids), then you have to make a mapping yourself. The info in the follwoing thread should help: md.chem.rug.nl/index.php/component/kunen...pping-a-new-molecule

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3 years 1 month ago #8819 by Pim
Replied by Pim on topic Oleic acid backmap
I have previously backmapped oleic acid from Martini to Charmm using the default backward script:

flags: -f backmap.gro -o aa_charmm.gro -to charmm36 -p topol.top

Note that backmap.gro is the endpoint of the martini simulation of a number of oleic acid CG molecules. Martini to charmm of OLEO should work (maybe it's your residue name).

the coordinates look like this:

Generated by trjconv : Martini system from 1f6r_mod.pdb t= 652000.00000
1335
124OAC COO 1 5.075 7.674 7.918
124OAC ASP 2 4.968 7.671 7.943
124OAC C1 3 5.271 7.685 7.498
124OAC D1 4 5.287 7.420 7.186
124OAC C2 5 5.374 7.021 7.274
124OAC C3 6 5.436 6.618 7.164
125OAC COO 7 6.075 5.362 8.486
125OAC ASP 8 6.030 5.362 8.386
125OAC C1 9 6.347 5.542 8.191
125OAC D1 10 6.561 5.730 7.972
125OAC C2 11 6.411 5.906 7.700
125OAC C3 12 6.236 6.021 7.301
ETC x 34


in topol.top it looked like this:

[ moleculetype ]
; Name nrexcl
OLEO 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 OLEO rtp OLEO q -1.0
1 CL 1 OLEO C1 1 0.62 12.011 ; qtot 0.62
2 OCL 1 OLEO O1 2 -0.76 15.9994 ; qtot -0.14
3 OCL 1 OLEO O2 3 -0.76 15.9994 ; qtot -0.9
4 CTL2 1 OLEO C2 4 -0.28 12.011 ; qtot -1.18
5 HAL2 1 OLEO H2A 5 0.09 1.008 ; qtot -1.09
6 HAL2 1 OLEO H2B 6 0.09 1.008 ; qtot -1
7 CTL2 1 OLEO C3 7 -0.18 12.011 ; qtot -1.18
8 HAL2 1 OLEO H3A 8 0.09 1.008 ; qtot -1.09
9 HAL2 1 OLEO H3B 9 0.09 1.008 ; qtot -1
10 CTL2 1 OLEO C4 10 -0.18 12.011 ; qtot -1.18
11 HAL2 1 OLEO H4A 11 0.09 1.008 ; qtot -1.09
12 HAL2 1 OLEO H4B 12 0.09 1.008 ; qtot -1
13 CTL2 1 OLEO C5 13 -0.18 12.011 ; qtot -1.18
14 HAL2 1 OLEO H5A 14 0.09 1.008 ; qtot -1.09
15 HAL2 1 OLEO H5B 15 0.09 1.008 ; qtot -1
16 CTL2 1 OLEO C6 16 -0.18 12.011 ; qtot -1.18
17 HAL2 1 OLEO H6A 17 0.09 1.008 ; qtot -1.09
18 HAL2 1 OLEO H6B 18 0.09 1.008 ; qtot -1
19 CTL2 1 OLEO C7 19 -0.18 12.011 ; qtot -1.18
20 HAL2 1 OLEO H7A 20 0.09 1.008 ; qtot -1.09
21 HAL2 1 OLEO H7B 21 0.09 1.008 ; qtot -1
22 CTL2 1 OLEO C8 22 -0.18 12.011 ; qtot -1.18
23 HAL2 1 OLEO H8A 23 0.09 1.008 ; qtot -1.09
24 HAL2 1 OLEO H8B 24 0.09 1.008 ; qtot -1
25 CEL1 1 OLEO C9 25 -0.15 12.011 ; qtot -1.15
26 HEL1 1 OLEO H9A 26 0.15 1.008 ; qtot -1
27 CEL1 1 OLEO C10 27 -0.15 12.011 ; qtot -1.15
28 HEL1 1 OLEO H10A 28 0.15 1.008 ; qtot -1
29 CTL2 1 OLEO C11 29 -0.18 12.011 ; qtot -1.18
30 HAL2 1 OLEO H11A 30 0.09 1.008 ; qtot -1.09
31 HAL2 1 OLEO H11B 31 0.09 1.008 ; qtot -1
32 CTL2 1 OLEO C12 32 -0.18 12.011 ; qtot -1.18
33 HAL2 1 OLEO H12A 33 0.09 1.008 ; qtot -1.09
34 HAL2 1 OLEO H12B 34 0.09 1.008 ; qtot -1
35 CTL2 1 OLEO C13 35 -0.18 12.011 ; qtot -1.18
36 HAL2 1 OLEO H13A 36 0.09 1.008 ; qtot -1.09
37 HAL2 1 OLEO H13B 37 0.09 1.008 ; qtot -1
38 CTL2 1 OLEO C14 38 -0.18 12.011 ; qtot -1.18
39 HAL2 1 OLEO H14A 39 0.09 1.008 ; qtot -1.09
40 HAL2 1 OLEO H14B 40 0.09 1.008 ; qtot -1
41 CTL2 1 OLEO C15 41 -0.18 12.011 ; qtot -1.18
42 HAL2 1 OLEO H15A 42 0.09 1.008 ; qtot -1.09
43 HAL2 1 OLEO H15B 43 0.09 1.008 ; qtot -1
44 CTL2 1 OLEO C16 44 -0.18 12.011 ; qtot -1.18
45 HAL2 1 OLEO H16A 45 0.09 1.008 ; qtot -1.09
46 HAL2 1 OLEO H16B 46 0.09 1.008 ; qtot -1
47 CTL2 1 OLEO C17 47 -0.18 12.011 ; qtot -1.18
48 HAL2 1 OLEO H17A 48 0.09 1.008 ; qtot -1.09
49 HAL2 1 OLEO H17B 49 0.09 1.008 ; qtot -1
50 CTL3 1 OLEO C18 50 -0.27 12.011 ; qtot -1.27
51 HAL3 1 OLEO H18A 51 0.09 1.008 ; qtot -1.18
52 HAL3 1 OLEO H18B 52 0.09 1.008 ; qtot -1.09
53 HAL3 1 OLEO H18C 53 0.09 1.008 ; qtot -1

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
4 5 1
4 6 1
4 7 1
7 8 1
7 9 1
7 10 1
10 11 1
10 12 1
10 13 1
13 14 1
13 15 1
13 16 1
16 17 1
16 18 1
16 19 1
19 20 1
19 21 1
19 22 1
22 23 1
22 24 1
22 25 1
25 26 1
25 27 1
27 28 1
27 29 1
29 30 1
29 31 1
29 32 1
32 33 1
32 34 1
32 35 1
35 36 1
35 37 1
35 38 1
38 39 1
38 40 1
38 41 1
41 42 1
41 43 1
41 44 1
44 45 1
44 46 1
44 47 1
47 48 1
47 49 1
47 50 1
50 51 1
50 52 1
50 53 1

[ pairs ]
ETC

ETC

ETC

[ molecules ]
; Compound #mols
OLEO 36

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3 years 1 month ago #8825 by bellafrizzo
Replied by bellafrizzo on topic Oleic acid backmap
Thank you pim for your input.
Can I ask you for CG oleic acid topology?

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3 years 1 month ago #8826 by Pim
Replied by Pim on topic Oleic acid backmap
We published the work here chemistry-europe.onlinelibrary.wiley.com....1002/cbic.201700496 , but OA was not the focus.

Notice that we used the polarisable Martini force field, which shows in the dummy particle in the deprotonated OA topology below

Neutral OA:
[ moleculetype ]
; molname nrexcl
OAN 1

[ atoms ]
; id type resnr residu atom cgnr charge mass
1 P4 1 OAN COO 1 0
2 C1 1 OAN C1 2 0
3 C4 1 OAN D1 3 0
4 C1 1 OAN C2 4 0
5 C1 1 OAN C3 5 0

[ bonds ]
; i j funct length force.c.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.47 1250
4 5 1 0.47 1250

[ angles ]
; i j k funct angle force.c.
1 2 3 2 180.0 25.0
2 3 4 2 120.0 45.0
3 4 5 2 180.0 25.0


deprotonated OA:
[ moleculetype ]
; molname nrexcl
OAC 1

[ atoms ]
; id type resnr residu atom cgnr charge mass
1 Qa 1 OAC COO 1 0
2 D 1 OAC ASP 2 -1
3 C1 1 OAC C1 2 0
4 C4 1 OAC D1 3 0
5 C1 1 OAC C2 4 0
6 C1 1 OAC C3 5 0

[ bonds ]
; i j funct length force.c.
1 3 1 0.47 1250
3 4 1 0.47 1250
4 5 1 0.47 1250
5 6 1 0.47 1250

[ angles ]
; i j k funct angle force.c.
1 3 4 2 180.0 25.0
3 4 5 2 120.0 45.0
4 5 6 2 180.0 25.0

[constraints]
; i j funct length
1 2 1 0.11

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3 years 1 month ago #8827 by bellafrizzo
Replied by bellafrizzo on topic Oleic acid backmap
If I had to do deprotonation free energy calculations I should have the same number of beads in both the neutral and charged form. Can I simply add the dummy atom to the neutral topology?

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3 years 1 month ago #8828 by Pim
Replied by Pim on topic Oleic acid backmap
Maybe don't use the polarisable version of the charged OA

You can find the topology for fatty acid head groups in general with examples here: cgmartini.nl/index.php/force-field-param...s/lipids/fatty-acids , it was also the basis for OA, just with a shorter tail.

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3 years 1 month ago #8833 by bellafrizzo
Replied by bellafrizzo on topic Oleic acid backmap
Do you have the backmap file by any chance?
However OLEO is deprecated, now it's OLEP the CHARMM topology for oleic acid. Just in case, can you also send me the full topology of OLEO as there exists no more.

Cheers
Matteo

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