Metal Atoms in PDB not properly recognized #2265
Description
Expected behavior
I expect
In [1]: import MDAnalysis as mda
In [2]: u = mda.Universe("example.pdb")
to work with the PDB file below.
Actual behavior
The following warnings are issued:
/users/lina3015/software/python/mdanalysis-develop/package/MDAnalysis/topology/guessers.py:73: UserWarning: Failed to guess the mass for the following atom types: Ca
warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
/users/lina3015/software/python/mdanalysis-develop/package/MDAnalysis/topology/guessers.py:73: UserWarning: Failed to guess the mass for the following atom types: Fe
warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
/users/lina3015/software/python/mdanalysis-develop/package/MDAnalysis/topology/guessers.py:73: UserWarning: Failed to guess the mass for the following atom types: Mg
warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
The problem comes from the fact that the name of the atoms are Mg, Fe, Ca instead of MG, FE, CA. Open Babel 2.4.1 outputs the name of the elements with the second letter in lower case.
The problem is discussed in Issue #1808.
Code to reproduce the behavior
PDB file:
HEADER Example
SEQRES 1 A 3 SER LYS GLY
ATOM 1 N SER A 2 13.761 13.879 -11.601 1.00 66.03 N
ATOM 2 HN1 SER A 2 12.949 13.271 -11.831 1.00 0.00 H
ATOM 3 HN2 SER A 2 14.536 13.296 -11.225 1.00 0.00 H
ATOM 4 HN3 SER A 2 13.478 14.583 -10.889 1.00 0.00 H
ATOM 5 CA SER A 2 14.219 14.576 -12.829 1.00 65.42 C
ATOM 6 HA SER A 2 14.524 13.844 -13.577 1.00 0.00 H
ATOM 7 C SER A 2 15.409 15.463 -12.478 1.00 64.57 C
ATOM 8 O SER A 2 16.554 15.049 -12.613 1.00 64.91 O
ATOM 9 CB SER A 2 13.078 15.409 -13.424 1.00 66.10 C
ATOM 10 HB1 SER A 2 12.909 16.282 -12.794 1.00 0.00 H
ATOM 11 HB2 SER A 2 12.173 14.803 -13.453 1.00 0.00 H
ATOM 12 OG SER A 2 13.388 15.841 -14.740 1.00 67.19 O
ATOM 13 HG SER A 2 12.635 16.375 -15.097 1.00 0.00 H
ATOM 14 N LYS A 3 15.133 16.673 -12.004 1.00 63.15 N
ATOM 15 H LYS A 3 14.140 16.965 -11.905 1.00 0.00 H
ATOM 16 CA LYS A 3 16.189 17.600 -11.619 1.00 61.61 C
ATOM 17 HA LYS A 3 17.177 17.202 -11.851 1.00 0.00 H
ATOM 18 C LYS A 3 16.032 17.823 -10.119 1.00 59.63 C
ATOM 19 O LYS A 3 16.667 17.140 -9.322 1.00 59.93 O
ATOM 20 CB LYS A 3 16.053 18.916 -12.392 1.00 62.69 C
ATOM 21 HB1 LYS A 3 15.627 18.694 -13.371 1.00 0.00 H
ATOM 22 HB2 LYS A 3 15.374 19.566 -11.841 1.00 0.00 H
ATOM 23 CG LYS A 3 17.362 19.663 -12.601 1.00 63.33 C
ATOM 24 HG1 LYS A 3 17.713 20.040 -11.641 1.00 0.00 H
ATOM 25 HG2 LYS A 3 18.102 18.976 -13.013 1.00 0.00 H
ATOM 26 CD LYS A 3 17.183 20.833 -13.559 1.00 64.34 C
ATOM 27 HD1 LYS A 3 16.514 21.561 -13.099 1.00 0.00 H
ATOM 28 HD2 LYS A 3 18.155 21.294 -13.732 1.00 0.00 H
ATOM 29 CE LYS A 3 16.593 20.409 -14.911 1.00 65.03 C
ATOM 30 HE1 LYS A 3 16.367 21.308 -15.484 1.00 0.00 H
ATOM 31 HE2 LYS A 3 15.672 19.857 -14.725 1.00 0.00 H
ATOM 32 NZ LYS A 3 17.501 19.548 -15.727 1.00 65.45 N
ATOM 33 HZ1 LYS A 3 18.382 20.064 -15.924 1.00 0.00 H
ATOM 34 HZ2 LYS A 3 17.718 18.678 -15.200 1.00 0.00 H
ATOM 35 HZ3 LYS A 3 17.033 19.304 -16.623 1.00 0.00 H
ATOM 36 N GLY A 4 15.116 18.721 -9.756 1.00 56.92 N
ATOM 37 H GLY A 4 14.586 19.222 -10.498 1.00 0.00 H
ATOM 38 CA GLY A 4 14.827 19.029 -8.362 1.00 53.00 C
ATOM 39 HA1 GLY A 4 14.484 20.063 -8.318 1.00 0.00 H
ATOM 40 HA2 GLY A 4 14.024 18.367 -8.038 1.00 0.00 H
ATOM 41 C GLY A 4 15.964 18.883 -7.376 1.00 49.65 C
ATOM 42 O GLY A 4 16.115 17.829 -6.749 1.00 50.49 O
TER
HETATM 5935 MG MG 1 20.414 28.113 14.934 1.00 25.89 Mg
HETATM 5936 O HOH 2 20.617 18.139 -10.469 1.00 44.84 O
HETATM 5937 O HOH 3 19.500 17.550 -12.901 1.00 49.35 O
HETATM 5938 O HOH 4 13.990 17.613 -4.873 1.00 38.69 O
HETATM 6932 FE FE 1 7.237 -13.445 41.879 1.00 16.53 Fe
HETATM 6933 O HOH 2 12.331 -25.176 49.589 1.00 11.03 O
HETATM 6934 O HOH 3 0.846 -28.056 24.965 1.00 3.98 O
HETATM 6935 O HOH 4 -1.805 -28.400 30.994 1.00 7.38 O
HETATM 3744 CA CA 1 18.911 11.652 7.836 1.00 2.33 Ca
HETATM 3745 CA CA 2 18.013 3.000 21.617 1.00 13.46 Ca
HETATM 3746 O HOH 3 19.129 20.805 2.497 1.00 13.12 O
HETATM 3747 O HOH 4 10.694 18.824 22.901 1.00 14.21 O
HETATM 3748 O HOH 5 24.830 32.697 7.145 1.00 17.46 O
END
Currently version of MDAnalysis
- Which version are you using? 0.19.3-dev
- Which version of Python (
python -V)? Python 3.7.3 - Which operating system? Linux Ubuntu 18/macOS 10.14