Errors in Data file.

I have some questions and send e-mail again.

I received reply from LAMMPS users and fixed some erros in my data file(data.dna).

But It is error again and I have some difficulties.

It is “ERROR on proc 0 : Needed bonus data not in data file (read_data.cpp : 1304)”

How can I do to fix my data and input file?

I attach them below.

------------------------------------------------------data.dna--------------------------------------------------------------------------------------------

LAMMPS Coarse-grained DNA Description

60 atoms
58 bonds
75 angles
74 dihedrals
18 impropers
20 ellipsoids

6 atom types
6 bond types
10 angle types
10 dihedral types
4 improper types

-10.000000 150.00000 xlo xhi
-10.000000 10.000000 ylo yhi
-10.000000 150.00000 zlo zhi

Masses

1 132.120
2 236.920
3 134.100
4 110.100
5 150.100
6 125.100

Atoms

1 ellispoid 3 1 4.055740 2.021384 0.000000 -5.567462
2 sphere 1 1.8836 62.719604 -0.000050 0.000000 -2.709000
3 sphere 2 5.4078 4.752750 0.000000 0.000000 1.872000
4 ellispoid 4 1 2.795548 7.100604 0.000000 0.875086
5 sphere 1 1.8836 62.719604 4.896969 0.000000 3.603280
6 sphere 2 5.4078 4.752750 4.896969 0.000000 8.184280
7 ellispoid 5 1 2.747045 13.162987 0.000000 8.723736
8 sphere 1 1.8836 62.719604 9.794810 0.000000 9.913092
9 sphere 2 5.4078 4.752750 9.794810 0.000000 14.494092
10 ellispoid 6 1 2.448848 16.684062 0.000000 13.762072
11 sphere 1 1.8836 62.719604 14.691471 0.000000 16.226244
12 sphere 2 5.4078 4.752750 14.691471 0.000000 20.807244
13 ellispoid 3 1 4.055740 21.788316 0.000000 19.815075
14 sphere 1 1.8836 62.719604 19.588421 0.000000 22.538577
15 sphere 2 5.4078 4.752750 19.588422 0.000000 27.119577
16 ellispoid 4 1 2.795548 26.406274 0.000000 26.472805
17 sphere 1 1.8836 62.719604 24.485372 0.000000 28.850910
18 sphere 2 5.4078 4.752750 24.485372 0.000000 33.431910
19 ellispoid 5 1 2.747045 31.628052 0.000000 32.385495
20 sphere 1 1.8836 62.719604 29.382322 0.000000 35.163243
21 sphere 2 5.4078 4.752750 29.382323 0.000000 39.744243
22 ellispoid 6 1 2.448848 36.271575 0.000000 39.012223
23 sphere 1 1.8836 62.719604 34.278983 0.000000 41.476395
24 sphere 2 5.4078 4.752750 34.278984 0.000000 46.057395
25 ellispoid 3 1 4.055740 41.375829 0.000000 45.065226
26 sphere 1 1.8836 62.719604 39.175934 0.000000 47.788728
27 sphere 2 5.4078 4.752750 39.175934 0.000000 52.369728
28 ellispoid 4 1 2.795548 45.993786 0.000000 51.722956
29 sphere 1 1.8836 62.719604 44.072884 0.000000 54.101061
30 sphere 2 5.4078 4.752750 44.072885 0.000000 58.682061
31 ellispoid 5 1 2.747045 51.214343 0.000000 57.634659
32 sphere 1 1.8836 62.719604 48.969835 0.000000 60.413394
33 sphere 2 5.4078 4.752750 48.969835 0.000000 64.994394
34 ellispoid 6 1 2.448848 55.859087 0.000000 64.262374
35 sphere 1 1.8836 62.719604 53.866496 0.000000 66.726546
36 sphere 2 5.4078 4.752750 53.866496 0.000000 71.307546
37 ellispoid 3 1 4.055740 60.963341 0.000000 70.315376
38 sphere 1 1.8836 62.719604 58.763446 0.000000 73.038879
39 sphere 2 5.4078 4.752750 58.763447 0.000000 77.619879
40 ellispoid 4 1 2.795548 65.583208 0.000000 76.971410
41 sphere 1 1.8836 62.719604 63.661287 0.000000 79.348691
42 sphere 2 5.4078 4.752750 63.661287 0.000000 83.929691
43 ellispoid 5 1 2.747045 70.802746 0.000000 82.882290
44 sphere 1 1.8836 62.719604 68.558238 0.000000 85.661024
45 sphere 2 5.4078 4.752750 68.558238 0.000000 90.242024
46 ellispoid 6 1 2.448848 75.447490 0.000000 89.510004
47 sphere 1 1.8836 62.719604 73.454899 0.000000 91.974176
48 sphere 2 5.4078 4.752750 73.454899 0.000000 96.555176
49 ellispoid 3 1 4.055740 80.551744 0.000000 95.563007
50 sphere 1 1.8836 62.719604 78.351849 0.000000 98.286509
51 sphere 2 5.4078 4.752750 78.351849 0.000000 102.867509
52 ellispoid 4 1 2.795548 85.170747 0.000000 102.221581
53 sphere 1 1.8836 62.719604 83.248800 0.000000 104.598842
54 sphere 2 5.4078 4.752750 83.248800 0.000000 109.179842
55 ellispoid 5 1 2.747045 90.390259 0.000000 108.132441
56 sphere 1 1.8836 62.719604 88.145750 0.000000 110.911175
57 sphere 2 5.4078 4.752750 88.145750 0.000000 115.492170
58 ellispoid 6 1 2.448848 96.091478 0.000000 116.360756
59 sphere 1 1.8836 62.719604 93.042411 0.000000 117.224327

Bonds

1 3 1 2
2 5 2 3
3 6 3 5
4 1 5 4
5 5 5 6
6 6 6 8
7 4 8 7
8 5 8 9
9 6 9 11
10 2 11 10
11 5 11 12
12 6 12 14
13 3 14 13
14 5 14 15
15 6 15 17
16 1 17 16
17 5 17 18
18 6 18 20
19 4 20 19
20 5 20 21
21 6 21 23
22 2 23 22
23 5 23 24
24 6 24 26
25 3 26 25
26 5 26 27
27 6 27 29
28 1 29 28
29 5 29 30
30 6 30 32
31 4 32 31
32 5 32 33
33 6 33 35
34 2 35 34
35 5 35 36
36 6 36 38
37 3 38 37
38 5 38 39
39 6 39 41
40 1 41 40
41 5 41 42
42 6 42 44
43 4 44 43
44 5 44 45
45 6 45 47
46 2 47 46
47 5 47 48
48 6 48 50
49 3 50 49
50 5 50 51
51 6 51 53
52 1 53 52
53 5 53 54
54 6 54 56
55 4 56 55
56 5 56 57
57 6 57 59
58 2 59 58

Angles

1 5 1 2 3
2 4 2 3 5
3 9 3 5 4
4 1 3 5 6
5 6 4 5 6
6 4 5 6 8
7 2 6 8 7
8 1 6 8 9
9 8 7 8 9
10 4 8 9 11
11 10 9 11 10
12 1 9 11 12
13 7 10 11 12
14 4 11 12 14
15 3 12 14 13
16 1 12 14 15
17 5 13 14 15
18 4 14 15 17
19 9 15 17 16
20 1 15 17 18
21 6 16 17 18
22 4 17 18 20
23 2 18 20 19
24 1 18 20 21
25 8 19 20 21
26 4 20 21 23
27 10 21 23 22
28 1 21 23 24
29 7 22 23 24
30 4 23 24 26
31 3 24 26 25
32 1 24 26 27
33 5 25 26 27
34 4 26 27 29
35 9 27 29 28
36 1 27 29 30
37 6 28 29 30
38 4 29 30 32
39 2 30 32 31
40 1 30 32 33
41 8 31 32 33
42 4 32 33 35
43 10 33 35 34
44 1 33 35 36
45 7 34 35 36
46 4 35 36 38
47 3 36 38 37
48 1 36 38 39
49 5 37 38 39
50 4 38 39 41
51 9 39 41 40
52 1 39 41 42
53 6 40 41 42
54 4 41 42 44
55 2 42 44 43
56 1 42 44 45
57 8 43 44 45
58 4 44 45 47
59 10 45 47 46
60 1 45 47 48
61 7 46 47 48
62 4 47 48 50
63 3 48 50 49
64 1 48 50 51
65 5 49 50 51
66 4 50 51 53
67 9 51 53 52
68 1 51 53 54
69 6 52 53 54
70 4 53 54 56
71 2 54 56 55
72 1 54 56 57
73 8 55 56 57
74 4 56 57 59
75 10 57 59 58

Dihedrals

1 1 1 2 3 5
2 5 5 3 2 1
3 10 2 3 5 6
4 9 3 5 6 8
5 2 4 5 6 8
6 6 8 6 5 4
7 10 5 6 8 9
8 9 6 8 9 11
9 3 7 8 9 11
10 7 11 9 8 7
11 10 8 9 11 12
12 9 9 11 12 14
13 4 10 11 12 14
14 8 14 12 11 10
15 10 11 12 14 15
16 9 12 14 15 17
17 1 13 14 15 17
18 5 17 15 14 13
19 10 14 15 17 18
20 9 15 17 18 20
21 2 16 17 18 20
22 6 20 18 17 16
23 10 17 18 20 21
24 9 18 20 21 23
25 3 19 20 21 23
26 7 23 21 20 19
27 10 20 21 23 24
28 9 21 23 24 26
29 4 22 23 24 26
30 8 26 24 23 22
31 10 23 24 26 27
32 9 24 26 27 29
33 1 25 26 27 29
34 5 29 27 26 25
35 10 26 27 29 30
36 9 27 29 30 31
37 2 28 29 30 32
38 6 32 30 29 28
39 10 29 30 32 33
40 9 30 32 33 35
41 3 31 32 33 35
42 7 35 33 32 31
43 10 32 33 35 36
44 9 33 35 36 38
45 4 34 35 36 38
46 8 38 36 35 34
47 10 35 36 38 39
48 9 36 38 39 41
49 1 37 38 39 41
50 5 41 39 38 37
51 10 38 39 41 42
52 9 39 41 42 44
53 2 40 41 42 44
54 6 44 42 41 40
55 10 41 42 44 45
56 9 42 44 45 47
57 3 43 44 45 47
58 7 47 45 44 43
59 10 44 45 47 48
60 9 45 47 48 50
61 4 46 47 48 50
62 8 50 48 47 46
63 10 47 48 50 51
64 9 48 50 51 53
65 1 49 50 51 53
66 5 53 51 50 49
67 10 50 51 53 54
68 9 51 53 54 56
69 2 52 53 54 56
70 6 56 54 53 52
71 10 53 54 56 58
72 9 54 56 57 59
73 3 55 56 57 59
74 7 59 57 56 55

Impropers

1 2 3 5 4 6
2 3 6 8 7 9
3 4 9 11 10 12
4 1 12 14 13 15
5 2 15 17 16 18
6 3 18 20 19 21
7 4 21 23 22 24
8 1 24 26 25 27
9 2 27 29 28 30
10 3 30 32 31 33
11 4 33 35 34 36
12 1 36 38 37 39
13 2 39 41 40 42
14 3 42 44 43 45
15 4 45 47 46 48
16 1 48 50 49 51
17 2 51 53 52 54
18 3 54 56 55 57

-------------------------------------------------------------------input.dna--------------------------------------------------------------------------------------------

DNA minimization

units real

atom_style hybrid molecular ellipsoid sphere

pair_style hybrid resquared 8.0 lj/cut/coul/cut 10.0 yukawa 6.8 10.0
bond_style harmonic
angle_style harmonic
dihedral_style class2
improper_style class2

Pair_coefficients

pair_coeff 1 1 lj/cut/coul/cut 1.0 1.0 1.0 1.0
pair_coeff 1 2 lj/cut/coul/cut 1.0 1.0 1.0 1.0
pair_coeff 1 3 resquared 0.25 2.0 1.0 1.0 1.0 3.6229 5.0023 1.4057
pair_coeff 1 4 resquared 0.25 2.0 1.0 1.0 1.0 2.5848 3.8092 1.3424
pair_coeff 1 5 resquared 0.25 2.0 1.0 1.0 1.0 4.3347 2.3717 0.7752
pair_coeff 1 6 resquared 0.25 2.0 1.0 1.0 1.0 3.6127 3.4088 0.9666
pair_coeff 2 2 yukawa 10.0
pair_coeff 2 3 resquared 729.67 4.2489 1.0 1.0 1.0 13.443 9.0257 2.6714
pair_coeff 2 4 resquared 534.84 4.1348 1.0 1.0 1.0 12.917 8.0570 3.5227
pair_coeff 2 5 resquared 244.45 4.1409 1.0 1.0 1.0 8.7902 4.1412 1.7311
pair_coeff 2 6 resquared 934.79 4.2940 1.0 1.0 1.0 15.0740 12.8730 2.9361
pair_coeff 3 3 resquared 3455.0 3.5969 3.6229 5.0023 1.4057 3.6229 5.0023 1.4057
pair_coeff 3 4 resquared 17115.0 3.6915 4.3800 2.6585 2.4634 2.9957 7.8481 1.0379
pair_coeff 3 5 resquared 4188.0 3.8501 3.6178 2.8420 1.5088 3.5849 4.4283 0.6581
pair_coeff 3 6 resquared 6195.0 3.7700 3.7656 2.1395 1.6393 4.86454 5.5447 0.8189
pair_coeff 4 4 resquared 7826.0 3.9060 2.5848 3.8092 1.3424 2.5848 3.8092 1.3424
pair_coeff 4 5 resquared 3720.0 3.961 1.7108 3.6023 1.163 3.3655 2.4695 0.8089
pair_coeff 4 6 resquared 4839.0 3.8553 1.1875 6.3381 1.2818 5.5485 4.9745 0.9895
pair_coeff 5 5 resquared 4274.0 4.0250 4.3347 2.3717 0.7752 4.3347 2.3717 0.7752
pair_coeff 5 6 resquared 51144.0 3.8664 5.4026 0.8356 1.1117 5.5485 4.9745 0.9895
pair_coeff 6 6 resquared 2347.0 3.8096 3.6127 3.4088 0.9666 3.6127 3.4088 0.9666

bond_coeff 1 harmonic 330.800000 3.057000
bond_coeff 2 harmonic 323.400000 3.169000
bond_coeff 3 harmonic 229.200000 3.501000
bond_coeff 4 harmonic 186.500000 3.572000
bond_coeff 5 harmonic 40.4500000 4.581000
bond_coeff 6 harmonic 5.59600000 5.194000

angle_coeff 1 9.755000 80.557900
angle_coeff 2 5.645000 110.351700
angle_coeff 3 3.925000 104.794000
angle_coeff 4 1.726500 110.122500
angle_coeff 5 12.09500 162.147100
angle_coeff 6 10.34500 156.646700
angle_coeff 7 14.06000 155.443500
angle_coeff 8 16.06000 161.001200
angle_coeff 9 16.28500 94.652700
angle_coeff 10 32.79000 85.829100

dihedral_coeff 1 class2 -0.090000 -1.410000 0.030000 0.800000 -0.050000 -4.000000
dihedral_coeff 2 class2 -0.100000 -1.260000 0.100000 -0.020000 -0.060000 -8.300000
dihedral_coeff 3 class2 -0.100000 -0.790000 -0.040000 -1.500000 -0.080000 -3.900000
dihedral_coeff 4 class2 -0.110000 -0.700000 -0.170000 1.850000 0.070000 -6.700000
dihedral_coeff 5 class2 -0.130000 -1.620000 -0.260000 1.850000 -0.050000 -0.700000
dihedral_coeff 6 class2 -0.070000 -0.900000 -0.220000 -0.720000 -0.050000 0.400000
dihedral_coeff 7 class2 -0.120000 -14.71000 -0.230000 -1.240000 -0.020000 -0.200000
dihedral_coeff 8 class2 -0.180000 0.200000 -0.220000 -0.480000 -0.140000 -0.100000
dihedral_coeff 9 class2 0.100000 0.000000 0.150000 2.440000 0.210000 2.170000
dihedral_coeff 10 class2 -0.080000 8.000000 -0.200000 -1.500000 0.044000 -0.900000

improper_coeff 1 class2 -1.400000 -0.770000 -0.300000 -0.770000 -0.300000 -0.600000
improper_coeff 2 class2 -2.000000 -0.510000 -0.700000 -1.040000 -0.400000 -1.000000
improper_coeff 3 class2 2.3600000 1.970000 0.000000 0.000000 0.000000 0.000000
improper_coeff 4 class2 2.6600000 1.620000 0.000000 0.000000 0.000000 0.000000

#kspace_style pppm 0.0001

read_data data.dna

neighbor 2.0 bin
neigh_modify delay 5

timestep 2.0
run_style respa 5 2 2 2 2 bond 1 angle 2 dihedral 3 improper 4 pair 5

thermo_style multi
thermo 50

fix 1 all langevin 295.0 295.0 1000.0 49879 omega yes

group dna type <= 6
dump 1 dna atom 10 dump.peptide

run 1000

minimize 0.0001 0.01 1000 10000

I've never tried using spheres or ellipsoids, but when you run across
an error and don't know what it means, check here:
http://lammps.sandia.gov/doc/Section_errors.html

In your case:
"Needed bonus data not in data file
    Some atom styles require bonus data. See the read_data doc page
for details. "

The "docs" it is referring to are located here (The error refers to
the data file.):

http://lammps.sandia.gov/doc/read_data.html

It says:
"Additional attributes must be defined for each ellipsoid in the
Ellipsoids section."

I think it means that you need to add a new section to your data file
(The "Ellipsoids" section. See link above, and scroll down.)

Hope this helps

Andrew

I am curious:

How do you control the orientation of the ellipsoids in your DNA
molecule? (See attached figure?) Are the ellipsoids free to spin?
Do you attempt to keep the ellipsoid's principle axis parallel to the
C1'- base bond? (This is the "theta" angle.)

Is there a way to do this in LAMMPS?

Cheers
Andrew

bonded_ellipsoids.jpg

bonded_ellipsoids.svg