Reading selection error - sele.dat not accepted when using .pdb file in -coords
This is the output of the command mimicpy prepqm -top topol.top -coords QMframe.pdb -sele QMatoms.dat
:
***** MiMiCPy *****
For more information type mimicpy [subcommand] --help
=====> Running prepqm <=====
**Reading topology**
**Reading coordinates** |Done
Reading selection from QMatoms.dat
Wrote Gromacs index file to index.ndx
Traceback (most recent call last):
File "/p/usersoftware/ias-5/BIN/JURECA-DC/MiMiC/01.11.2022-rc/mimicpy_venv/bin/mimicpy", line 11, in <module>
load_entry_point('mimicpy==0.1.0', 'console_scripts', 'mimicpy')()
File "/p/usersoftware/ias-5/BIN/JURECA-DC/MiMiC/01.11.2022-rc/mimicpy_venv/lib64/python3.6/site-packages/mimicpy/__main__.py", line 592, in main
args.func(args)
File "/p/usersoftware/ias-5/BIN/JURECA-DC/MiMiC/01.11.2022-rc/mimicpy_venv/lib64/python3.6/site-packages/mimicpy/__main__.py", line 208, in prepqm
do_prep()
File "/p/usersoftware/ias-5/BIN/JURECA-DC/MiMiC/01.11.2022-rc/mimicpy_venv/lib64/python3.6/site-packages/mimicpy/__main__.py", line 177, in do_prep
args.path, args.q, args.pp)
File "/p/usersoftware/ias-5/BIN/JURECA-DC/MiMiC/01.11.2022-rc/mimicpy_venv/lib64/python3.6/site-packages/mimicpy/core/prepare.py", line 171, in get_mimic_input
sorted_qm_atoms = self.__qm_atoms.sort_values(by=['is_link', 'element']).reset_index()
File "/p/usersoftware/ias-5/BIN/JURECA-DC/MiMiC/01.11.2022-rc/mimicpy_venv/lib64/python3.6/site-packages/pandas/core/frame.py", line 5284, in sort_values
keys = [self._get_label_or_level_values(x, axis=axis) for x in by]
File "/p/usersoftware/ias-5/BIN/JURECA-DC/MiMiC/01.11.2022-rc/mimicpy_venv/lib64/python3.6/site-packages/pandas/core/frame.py", line 5284, in <listcomp>
keys = [self._get_label_or_level_values(x, axis=axis) for x in by]
File "/p/usersoftware/ias-5/BIN/JURECA-DC/MiMiC/01.11.2022-rc/mimicpy_venv/lib64/python3.6/site-packages/pandas/core/generic.py", line 1563, in _get_label_or_level_values
raise KeyError(key)
KeyError: 'element'
The program works properly if I manually select the atoms with the same QMframe.pdb file or if I use a .gro file with the sele.dat file as input.
Edited by Giuseppe Silvestri