Thanks Dave,
Yes I have successfully replicated the existing substructure match to get
the lists that would be autogenerated by GetBestRMS and am now working on
the permutations arising from the carboxylates. my code would work right
now if i only had one COO...
*Kind Regards*
Dr. Martin
Hi Martin,
Sorry, I forgot to 'Reply All' last night. I think you need to do a bit
more work than just map the carboxylate groups. Phenol maps onto itself
twice, going either way round the phenyl ring. GetBestRMS does this for
you, and reports the lower RMS. For benzoic acid, adding the
Update, the explicit or not charge is not relevant. that just determines
the behaviour of the AssignBondOrderstoTemplate. The behaviour is that
GetBestRMS does not consider a carboxylate as symmetric. Can anyone
suggest a workaround to treat as symmetric?
*Kind Regards*
Dr. Martin Watson
VP
Hi
I'm using GetBestRMS to score conformers in an sdf relative to a pdb
extracted sdf ligand using the snippet below. I get odd behaviour when the
molecule includes a carboxylic acid. depending on whether the charge is
explicitly defined in the sdf or not I get a different RMS which seems to
be
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