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UCL-CCS / TIES

Topology Superimposition based on joint graph traversal
MIT License
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Super impose ligands issue with oxazole,thiazole, and imidazole #323

Closed Oulfin closed 1 year ago

Oulfin commented 1 year ago

Hi again,

I just realized that when one wants to perform a transformation from oxazole, thiazole, or imidazole to just add a methyl, it crashes. However, when the same transformation is done using isoxazole, isothiazole, and pyrazole to a methyl, it works.

Do you know what is the possible issue?

Best,

Fail_superimpose

bieniekmateusz commented 1 year ago

Hi @Oulfin, I'll have some time later this week and will get back to you on this. Thanks

Oulfin commented 1 year ago

Hi @bieniekmateusz,

I found the error. In the "pair.py"

Line 391: if "Could not find bond parameter for:" in line: --> if "Could not find bond parameter for" in line:

Line 394: elif "Could not find angle parameter for:" in line: --> elif "Could not find angle parameter for" in line:

The problem was that it was not able to detect angle parameter from the leap.log and create the dummy angles parameter.

Thanks!

bieniekmateusz commented 1 year ago

Hi @Oulfin , apologies for the delay. I will look into this this weekend. This error occasionally showed up when the "antechamber" was too old or too new: because they changed the wording (See #319).

Would you be able to provide your files for the superimposition? I'll check the different options (like utilising the coordinates) etc. Thanks!

Oulfin commented 1 year ago

Hi,

Sorry for the late response, I was away. So far I could make it word by changing the wording. I did not get error after that.

Thanks!