Hello, I am new to Python RDKit, and I want to make conformers for TMA adsorbed to amorphous SiO2 (see attached), where only trimethylaluminum is altered but the SiO2 substrate is held fixed. I tried using the AllChem.ConstrainedEmbed(molecule, core, etc.) command with useTethers = true, but it gives me the following error:
Constrained conformer generation (via the coordMap argument) does not work with molecules that have multiple fragments. Do you have any idea how I could get around this, say by completing the molecule fragments without altering the existing geometry? Thanks so much for your help, and let me know if you need any other information. Best, Rob
ex1_TMAadsorption.xyz
Description: ex1_TMAadsorption.xyz
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