Run only with xTB?

[doohyunkwon]

Is it possible to calculate the energies if we don't have access to ORCA? I see on esnuel.org website that the energies may be calculated only using xTB. Trying to replicate the same energies launched from the command line, but I'm getting nonsensical numbers (just -inf).
I followed the README and was able to get everything set up besides ORCA.

This is the output I get from running the testmol job
Electrophilic sites:
['Amide', 'double_bond', 'double_bond', 'double_bond', 'double_bond', 'double_bond', 'double_bond', 'double_bond', 'double_bond', 'double_bond', 'dou
ble_bond', 'double_bond']
[9, 2, 7, 8, 10, 13, 14, 15, 16, 20, 22, 23]
[-inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf]
Nucleophilic sites:
['Amide', 'Amine', 'Phenol', 'Pyridine_like_nitrogen', 'double_bond', 'double_bond', 'double_bond', 'double_bond', 'double_bond', 'double_bond', 'dou
ble_bond', 'double_bond', 'double_bond', 'atom_with_lone_pair', 'atom_with_lone_pair', 'atom_with_lone_pair', 'atom_with_lone_pair']
[10, 6, 21, 7, 2, 8, 9, 13, 14, 15, 16, 20, 22, 1, 11, 17, 23]
[-inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf, -inf]
submitit INFO (2024-02-13 22:43:29,906) - Job completed successfully

Great work btw!

[NicolaiRee]

Hi Doo-Hyun Kwon,

Thanks for your interest in ESNUEL! So great to know a bit about some of the people trying/using this work.

For the moment, I have created a branch called esnuel-xtb, which removes all ORCA calls. This allows you to run ESNUEL based on GFN1-xTB energies similar to our web application.

Best wishes, Nicolai

[NicolaiRee]

TODO: Make a --xtb-only True/False flag in the CLI of the ESNUEL main branch.

[doohyunkwon]

Thank you for the quick update Nicolai!

I'm able to successfully replicate the results from the web application using the esnuel-xtb branch.

[NicolaiRee]

That's great to hear!

[tranJen]

@NicolaiRee I'm not sure if I'm running the same problem, but I got the same output.

I was trying to run the code in Jupyter notebook on google Colab with following code:
(I tried original and esnuel-xtb branch and it gave the same output)
calc_MAA_and_MCA('O=C1CCCC1', 'test')

Output:
Electrophilic sites:
Electrophilic sites:
['Ketone', 'double_bond']
[1, 0]
[-inf, -inf]
Nucleophilic sites:
['Ketone']
[0]
[-inf]
([[1, 0]],
[['Ketone', 'double_bond']],
[['CC1([O-])CCCC1', 'CO[C-]1CCCC1']],
[[-inf, -inf]],
[[[[None, 'test/reac01/conf01/gfn1/test_reac01_conf01_gfn1_opt.sdf'],
[None,
'test/reac01prodE01/conf02/gfn1/test_reac01prodE01_conf02_gfn1_opt.sdf']],
[[None, 'test/reac01/conf01/gfn1/test_reac01_conf01_gfn1_opt.sdf'],
[None,
'test/reac01prodE02/conf04/gfn1/test_reac01prodE02_conf04_gfn1_opt.sdf']]]],
[[0]],
[['Ketone']],
[['CO[C+]1CCCC1']],
[[-inf]],
[[[[None, 'test/reac01/conf01/gfn1/test_reac01_conf01_gfn1_opt.sdf'],
[None,
'test/reac01prodN01/conf05/gfn1/test_reac01prodN01_conf05_gfn1_opt.sdf']]]])

I tried this molecule on the website esnuel.org and it gave MAA value = 287.90 kJ/mol when only using xTB
Was I doing something wrong in my code? Please let me know if you need more information.

Thank you!

[NicolaiRee]

Hi @tranJen, I created a separate issue for your question. Please see #2.