Dear All, I would like to compute RMS values between conformers of the same molecule that are not aligned. Unfortunately, I can´t get along very well with the GetConformerRMS() function, it gives far too high RMS values even for conformers that are clearly (near-)identical as judged by visual inspection after alignment. I attach one example of 2 conformers of a molecule, that are near-identical. GetConformerRMS() returns an RMS value of 1.32 (with Hydrogens) and 0.70 (disregarding Hydrogens). GetBestRMS() returns an RMS value of 0.03 (with Hydrogens) and 0.02 (disregarding Hydrogens).
Clearly, the GetBestRMS() result is the one I´d expect (I am interested in the all-atom RMSDs with Hydrogens). I guess GetConformerRMS() cannot align the two conformers properly hence the high RMS value. My question is why not? The atom ordering and all bonds are exactly the same in both conformers. Why do I need the GetBestRMS() alignment of all possible permutations of matching atom orders in both conformers to get the alignment correct? I would like to avoid using GetBestRMS()as it is far too slow for my purposes (processing many molecules with many conformers). Many thanks for any hints, Anikó
confs.sdf
Description: confs.sdf
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