Issue when generating box.gro

User discussions
1

GROMACS version: 2022.2-spack
GROMACS modification: No

I’ve been trying to follow the tutorial shown at https://bioinformaticsreview.com/20200712/tutorial-md-simulation-of-a-protein-ligand-complex-using-gromacs/ to perform MD simulation in a protein-ligand complex.
After generating the complex.gro, I used the command “gmx editconf -f complex.gro -o box.gro -c -d 2.0 -bt dodecahedron” to define the solvation box. However, no coordinates are generated in the box.gro file (see below).

Gravel Rubs Often Many Awfully Cauterized Sores
8571
1SER N 1 nan nan nan
1SER H1 2 nan nan nan
1SER H2 3 nan nan nan
1SER H3 4 nan nan nan
1SER CA 5 nan nan nan
1SER HA 6 nan nan nan
1SER CB 7 nan nan nan
1SER HB1 8 nan nan nan
1SER HB2 9 nan nan nan
1SER OG 10 nan nan nan
1SER HG1 11 nan nan nan
1SER C 12 nan nan nan
1SER O 13 nan nan nan
2GLU N 14 nan nan nan
2GLU HN 15 nan nan nan
2GLU CA 16 nan nan nan
2GLU HA 17 nan nan nan
2GLU CB 18 nan nan nan
2GLU HB1 19 nan nan nan
2GLU HB2 20 nan nan nan
2GLU CG 21 nan nan nan
2GLU HG1 22 nan nan nan
2GLU HG2 23 nan nan nan
2GLU CD 24 nan nan nan
2GLU OE1 25 nan nan nan
2GLU OE2 26 nan nan nan
2GLU C 27 nan nan nan
2GLU O 28 nan nan nan
3VAL N 29 nan nan nan
3VAL HN 30 nan nan nan
3VAL CA 31 nan nan nan
3VAL HA 32 nan nan nan
3VAL CB 33 nan nan nan
3VAL HB 34 nan nan nan
3VAL CG1 35 nan nan nan
3VAL HG11 36 nan nan nan
3VAL HG12 37 nan nan nan
3VAL HG13 38 nan nan nan
3VAL CG2 39 nan nan nan
3VAL HG21 40 nan nan nan
3VAL HG22 41 nan nan nan
3VAL HG23 42 nan nan nan
3VAL C 43 nan nan nan
3VAL O 44 nan nan nan
4ALA N 45 nan nan nan
4ALA HN 46 nan nan nan
(…)

What could be the reason for this error?

Thank you!

2

Perhaps the coordinates in complex.gro are misformatted? Do they display properly in e.g. VMD and does the file conform to the required format and spacing?

3

The “complex.gro” file opens in ChimeraX normally. The error message shown is “Fatal error:
A coordinate in file box.gro does not contain a ‘.’”

The “complex.gro” is below.

Human Serum Albumin
8571
1SER N 1 -1.807 -1.590 2.592
1SER H1 2 -1.889 -1.601 2.648
1SER H2 3 -1.812 -1.652 2.514
1SER H3 4 -1.726 -1.612 2.647
1SER CA 5 -1.798 -1.449 2.544
1SER HA 6 -1.879 -1.434 2.488
1SER CB 7 -1.794 -1.352 2.662
1SER HB1 8 -1.880 -1.355 2.712
1SER HB2 9 -1.719 -1.374 2.723
1SER OG 10 -1.775 -1.219 2.617
1SER HG1 11 -1.773 -1.157 2.695
1SER C 12 -1.674 -1.428 2.457
1SER O 13 -1.564 -1.473 2.491
2GLU N 14 -1.692 -1.359 2.345
2GLU HN 15 -1.784 -1.325 2.323
2GLU CA 16 -1.583 -1.332 2.253
2GLU HA 17 -1.522 -1.412 2.256
2GLU CB 18 -1.638 -1.314 2.112
2GLU HB1 19 -1.705 -1.386 2.095
2GLU HB2 20 -1.683 -1.225 2.107
2GLU CG 21 -1.535 -1.320 2.001
2GLU HG1 22 -1.582 -1.308 1.913
2GLU HG2 23 -1.469 -1.245 2.014
2GLU CD 24 -1.459 -1.451 1.997
2GLU OE1 25 -1.507 -1.550 2.056
2GLU OE2 26 -1.350 -1.454 1.934
2GLU C 27 -1.508 -1.208 2.298
2GLU O 28 -1.385 -1.207 2.301
3VAL N 29 -1.581 -1.104 2.335
3VAL HN 30 -1.681 -1.110 2.331
3VAL CA 31 -1.519 -0.980 2.381
3VAL HA 32 -1.468 -0.949 2.301
3VAL CB 33 -1.623 -0.877 2.424
3VAL HB 34 -1.673 -0.910 2.504
3VAL CG1 35 -1.555 -0.746 2.461
3VAL HG11 36 -1.624 -0.679 2.489
3VAL HG12 37 -1.491 -0.761 2.536
3VAL HG13 38 -1.505 -0.711 2.381
3VAL CG2 39 -1.723 -0.856 2.314
3VAL HG21 40 -1.791 -0.788 2.342
3VAL HG22 41 -1.675 -0.822 2.232
3VAL HG23 42 -1.768 -0.942 2.293
3VAL C 43 -1.426 -1.006 2.499
3VAL O 44 -1.315 -0.953 2.505
4ALA N 45 -1.474 -1.086 2.594
4ALA HN 46 -1.565 -1.125 2.585
4ALA CA 47 -1.394 -1.118 2.711
4ALA HA 48 -1.374 -1.032 2.759
4ALA CB 49 -1.472 -1.210 2.803
4ALA HB1 50 -1.416 -1.232 2.884
4ALA HB2 51 -1.556 -1.165 2.832
4ALA HB3 52 -1.494 -1.295 2.755
4ALA C 53 -1.266 -1.185 2.664
4ALA O 54 -1.156 -1.145 2.701
5HIS N 55 -1.284 -1.288 2.581
5HIS HN 56 -1.377 -1.314 2.558
5HIS CA 57 -1.174 -1.366 2.523
5HIS HA 58 -1.142 -1.425 2.597
5HIS CB 59 -1.227 -1.445 2.403
5HIS HB1 60 -1.304 -1.501 2.433
5HIS HB2 61 -1.258 -1.380 2.333
5HIS ND1 62 -0.994 -1.502 2.326
5HIS CG 63 -1.127 -1.536 2.340
5HIS CE1 64 -0.930 -1.600 2.263
5HIS HE1 65 -0.833 -1.601 2.239
5HIS NE2 66 -1.017 -1.695 2.236
5HIS HE2 67 -0.997 -1.781 2.188
5HIS CD2 68 -1.141 -1.658 2.283
5HIS HD2 69 -1.225 -1.711 2.277
5HIS C 70 -1.059 -1.276 2.477
5HIS O 71 -0.948 -1.283 2.530
6ARG N 72 -1.088 -1.193 2.378
6ARG HN 73 -1.181 -1.192 2.342
6ARG CA 74 -0.989 -1.103 2.320
6ARG HA 75 -0.914 -1.163 2.294
6ARG CB 76 -1.052 -1.032 2.199
6ARG HB1 77 -1.125 -0.973 2.232
6ARG HB2 78 -0.981 -0.977 2.155
6ARG CG 79 -1.110 -1.129 2.097
6ARG HG1 80 -1.178 -1.186 2.141
6ARG HG2 81 -1.152 -1.076 2.023
6ARG CD 82 -1.002 -1.219 2.037
6ARG HD1 83 -0.942 -1.164 1.978
6ARG HD2 84 -0.949 -1.261 2.110
6ARG NE 85 -1.058 -1.327 1.955
6ARG HE 86 -1.157 -1.337 1.952
6ARG CZ 87 -0.985 -1.412 1.884
6ARG NH1 88 -0.852 -1.401 1.884
6ARG HH11 89 -0.807 -1.330 1.938
6ARG HH12 90 -0.797 -1.466 1.831
6ARG NH2 91 -1.043 -1.508 1.814
6ARG HH21 92 -1.143 -1.517 1.814
6ARG HH22 93 -0.988 -1.572 1.761
6ARG C 94 -0.932 -1.000 2.418
6ARG O 95 -0.813 -0.966 2.411
(…)
5.94821 8.71162 6.96949

4

Check to make sure the number of atoms on the second line is correct, and if necessary, start over in creating this file. If you need more help diagnosing the issue, please upload the complex.gro file so we can look at it.