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jensengroup / ESNUEL

Estimating Nucleophilicity and Electrophilicity with Automated Quantum Chemistry-Based Computations of Methyl Affinities
https://esnuel.org/
MIT License
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Run only with xTB? #1

Open doohyunkwon opened 9 months ago

doohyunkwon commented 9 months ago

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 commented 9 months ago

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 commented 9 months ago

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

doohyunkwon commented 9 months ago

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 commented 9 months ago

That's great to hear!

tranJen commented 4 months ago

@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 commented 4 months ago

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