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Description
Expected behavior
When I try to parse following gro file using MDAnalysis.Universe,
Example gro file
mCP
52
1LIG C00 1 1.382 1.369 3.583 0.0621 -0.1579 -0.3177
1LIG C01 2 1.516 1.408 3.551 0.2861 0.3115 -0.4733
1LIG C02 3 1.335 1.406 3.711 -0.1396 0.1043 -0.6418
1LIG C03 4 1.413 1.470 3.804 0.2561 0.2800 0.2722
1LIG C04 5 1.603 1.465 3.646 -0.9943 0.1843 -0.0949
1LIG C05 6 1.547 1.498 3.773 0.0720 0.3654 0.5643
1LIG H06 7 1.705 1.487 3.617 -2.1881 -1.6600 1.6244
1LIG H07 8 1.326 1.312 3.512 -0.1227 1.6765 3.4071
1LIG H08 9 1.373 1.505 3.904 -2.8380 0.2915 0.0254
1LIG H09 10 1.609 1.543 3.847 -0.9918 0.6125 0.1841
1LIG N0A 11 1.569 1.360 3.423 0.7252 0.4807 0.1006
1LIG N0B 12 1.199 1.378 3.753 0.0195 0.6945 -0.3455
1LIG C0C 13 1.511 1.382 3.298 -0.0718 0.0881 0.4777
1LIG C0D 14 1.693 1.291 3.403 -0.8847 0.5669 -0.3861
1LIG C0E 15 1.079 1.390 3.677 0.1428 -0.3040 -0.4933
1LIG C0F 16 1.157 1.323 3.880 -1.2695 0.3701 0.7727
1LIG C0G 17 0.967 1.354 3.754 0.1120 -0.1261 0.2826
1LIG C0H 18 1.019 1.302 3.872 0.6453 0.4619 -0.6466
1LIG C0I 19 1.706 1.270 3.258 -0.1344 0.4492 0.3150
1LIG C0J 20 1.595 1.327 3.198 -0.3651 0.3864 0.9254
1LIG C0K 21 1.563 1.348 3.060 0.0239 0.2715 1.5069
1LIG C0M 22 1.395 1.451 3.278 0.3359 0.8552 0.0206
1LIG C0N 23 1.820 1.205 3.211 -0.8869 0.1811 0.0699
1LIG C0O 24 1.784 1.254 3.501 0.2992 -0.1149 -0.4235
1LIG C0P 25 1.084 1.464 3.558 0.0214 -0.0379 0.1615
1LIG C0Q 26 0.839 1.378 3.699 -0.0488 0.1386 -0.0709
1LIG C0R 27 1.239 1.285 3.989 0.3367 -0.1765 -0.0590
1LIG C0S 28 0.957 1.237 3.982 0.1652 0.3390 -0.8689
1LIG C0T 29 1.175 1.229 0.053 -0.1744 0.0147 -0.0595
1LIG C0U 30 1.035 1.198 0.045 -0.0222 0.4244 -0.4755
1LIG C0V 31 0.951 1.491 3.510 0.2775 -0.1529 0.3318
1LIG C0W 32 0.832 1.442 3.573 0.1285 -0.4091 -0.5051
1LIG C0X 33 1.440 1.413 3.035 0.0008 0.2347 -0.2036
1LIG C0Y 34 1.357 1.470 3.141 -0.4632 1.0063 -0.2381
1LIG C0Z 35 1.913 1.162 3.309 -0.7378 0.4248 -0.2854
1LIG C10 36 1.894 1.177 3.450 0.3427 0.6086 -0.1384
1LIG H11 37 1.835 1.181 3.105 -0.3026 -1.0577 1.3633
1LIG H12 38 1.990 1.094 3.274 0.8838 -3.0362 -3.3538
1LIG H13 39 1.767 1.282 3.603 1.5678 0.4610 0.1510
1LIG H14 40 1.965 1.147 3.523 2.8042 0.8007 1.6468
1LIG H15 41 1.618 1.301 2.980 -2.3607 -1.0238 1.5835
1LIG H16 42 1.411 1.434 2.933 -0.4707 -0.3738 -0.3861
1LIG H17 43 1.353 1.498 3.365 -0.1283 2.4331 0.5324
1LIG H18 44 1.263 1.521 3.117 -2.4200 -1.8720 1.1648
1LIG H19 45 0.952 1.545 3.415 0.9236 -0.1758 0.1509
1LIG H1A 46 1.179 1.495 3.515 0.6316 0.7709 -1.4005
1LIG H1B 47 0.742 1.462 3.523 -0.4545 0.5913 -0.5083
1LIG H1C 48 0.749 1.363 3.760 0.4201 1.1105 2.4743
1LIG H1D 49 1.347 1.280 3.982 -1.0797 0.6533 0.4476
1LIG H1E 50 1.230 1.205 0.144 0.4106 1.5828 1.9807
1LIG H1F 51 0.995 1.147 0.137 1.2287 0.4955 1.6285
1LIG H1G 52 0.847 1.214 3.994 -0.4029 -1.2299 1.5198
type of atoms must be following:
Expected result
'C'
'C'
'C'
'C'
'C'
'C'
'H'
'H'
'H'
'H'
'N'
'N'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
Actual behavior
However, what I actually get is:
Actual result
'C'
'C'
'C'
'C'
'C'
'C'
'H'
'H'
'H'
'H'
'NA'
'N'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'C'
'CS'
'C'
'CU'
'C'
'C'
'C'
'C'
'C'
'C'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
'H'
Code to reproduce the behavior
import MDAnalysis as mda
gro = mda.Universe('prod.gro') #Example gro file
mol = gro.residues[0]
for atom in mol.atoms:
atom.type
Current version of MDAnalysis
- MDAnalysis : 2.5.0
- Python : 3.11.3
- operating system : Rocky Linux