Open DCB0I opened 1 month ago
Hi,
Can you please be a little bit more specific which files have you run. Could you please share with me all the files in your input directory, and the output directory with the corresponding file created. I can deduce better what the problem is.
I am attaching the files here. Any kind of help will be very much appreciated.
On Fri, Jul 19, 2024 at 1:38 PM MatthijsHak @.***> wrote:
Hi,
Can you please be a little bit more specific which files have you run. Could you please share with me all the files in your input directory, and the output directory with the corresponding file created. I can deduce better what the problem is.
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You do not have any files related to Gaussian in your output/QM directory. I therefore believe that probably the configuration with Gaussian is not correct. You should obtain a single_point.log file in which the output of the QM calculation is written.
I followed the instructions as stated and within the folder containing the .pdb, .xyz and .ini file. Then I opened the terminal within it and activated the environment MetalDock and wrote metaldock -i file_name.ini. My system contains Gaussian v6. Do I have to specify the path directory somewhere.
The following environment variable should be set:
export g16root=/full/path/to/gaussian/g16
Could you verify if the path to the gaussian binary is correclty set?
OK can you tell me where to find this actually? When I call gv6 in the terminal, the application opens up by the way.
In your terminal you should type before executing Gaussian export g16root=/your/path/to/gaussian/g16 (where you change the path to the path to the g16 executable). To verify if it was successful, you can then type echo $g16root, and the terminal should then print the path that you have just set.
The path to gaussian is correctly as mentioned but still the error says like this : Traceback (most recent call last): File "/home/chemistry3/.conda/envs/MetalDock/lib/python3.8/site-packages/ase/io/extxyz.py", line 743, in read_xyz natoms = int(line) ValueError: invalid literal for int() with base 10: 'Open Babel 3.1.0 -- Sep 16 2021 -- 06:44:16\n'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/chemistry3/MetalDock/metaldock", line 6, in
To verify that ASE and Gaussian are correctly connected could you please create the following python script:
from ase import Atoms
from ase.calculators.gaussian import Gaussian
atoms = Atoms('H2', [[0, 0, 0], [0, 0, 0.74]])
atoms.calc = Gaussian(mem='1GB',
chk='MyJob.chk',
save=None,
method='b3lyp',
basis='6-31G',
scf='qc')
atoms.get_potential_energy()
And run the python script with the python of the MetalDock conda environment.
atoms = Atoms('H2', [[0,0,0], [0,0,0.74]]) atoms.calc = Gaussian(mem='1GB', ... chk='Testing.chk', ... save=None, ... method='b3lyp', ... basis='6-31G', ... scf='qc') atoms.get_potential_energy() -31.986361860985223
This appears to be working properly. However the error with the input file still persists and shows the same thing.
Okay great. I now understand that it has to do with your openbabel, and the error starts with the first line of code being executed. For some reason openbabel is incorrectly executed on your machine. Now the xyz file of your specify the following error:
Open Babel 3.1.0 -- Sep 16 2021 -- 06:44:16
Usage:
obabel [-i
If I install openbabel via conda install openbabel
, I obtain the following version:
Open Babel 3.1.0 -- Nov 30 2023 -- 20:44:30
Could you try to uninstall / remove openbabel from your conda environment and reinstall it.
This solved my problem however when I try using this on my experimental complex such an error shows up: GAUSSIAN REQUIRES A SINGLE POINT CALCULATION TO EXTRACT CM5 CHARGES
SINGLE POINT SUCCESSFULLY PERFORMED
SPACING BETWEEN GRID POINTS IS STANDARD SET TO 0.375 Å BOX SIZE MUST BE INTEGER GRID POINTS WHICH WAS NOT FOUND BOX SIZE SIDE ROUNDED UP AND SET TO 120.301 Å
Traceback (most recent call last):
File "/home/chemistry3/MetalDock/metaldock", line 6, in
Do you have the latest repository? It could be a bug from a earlier version.
I executed one of the example run and it ran just fine. However this is the message I am getting when I am using it for my complex and DNA (as the receptor).
I do not see the message.
I have 2 questions:
(MetalDock) chemistry3@fedora:~/MetalDock/examples/example_runs/vacancy_coordination_sphere/GAUSSIAN$ metaldock -i input.ini Traceback (most recent call last): File "/home/chemistry3/.conda/envs/MetalDock/lib/python3.8/site-packages/ase/io/extxyz.py", line 743, in read_xyz natoms = int(line) ValueError: invalid literal for int() with base 10: 'Open Babel 3.1.0 -- Sep 16 2021 -- 06:44:16\n'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/chemistry3/MetalDock/metaldock", line 6, in
main()
File "/home/chemistry3/MetalDock/src/metal_dock/main.py", line 18, in main
docking(par)
File "/home/chemistry3/MetalDock/src/metal_dock/docking.py", line 77, in docking
qm_dir, energy = g.gaussian_engine(xyz_file, par, output_dir)
File "/home/chemistry3/MetalDock/src/metal_dock/gaussian_engine.py", line 67, in gaussian_engine
gaussian_sp('output.xyz', var)
File "/home/chemistry3/MetalDock/src/metal_dock/gaussian_engine.py", line 182, in gaussian_sp
mol = read(xyz_file)
File "/home/chemistry3/.conda/envs/MetalDock/lib/python3.8/site-packages/ase/io/formats.py", line 736, in read
return next(_iread(filename, slice(index, None), format, io,
File "/home/chemistry3/.conda/envs/MetalDock/lib/python3.8/site-packages/ase/parallel.py", line 275, in new_generator
for result in generator(*args, *kwargs):
File "/home/chemistry3/.conda/envs/MetalDock/lib/python3.8/site-packages/ase/io/formats.py", line 803, in _iread
for dct in io.read(fd, args, kwargs):
File "/home/chemistry3/.conda/envs/MetalDock/lib/python3.8/site-packages/ase/io/formats.py", line 559, in wrap_read_function
for atoms in read(filename, index, kwargs):
File "/home/chemistry3/.conda/envs/MetalDock/lib/python3.8/site-packages/ase/io/extxyz.py", line 745, in read_xyz
raise XYZError('ase.io.extxyz: Expected xyz header but got: {}'
ase.io.extxyz.XYZError: ase.io.extxyz: Expected xyz header but got: invalid literal for int() with base 10: 'Open Babel 3.1.0 -- Sep 16 2021 -- 06:44:16\n'