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Allow multiple QM/MM link atoms on the same QM atom - #516
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Allow a QM atom to have more than one bond to the MM region, adding a link atom for each bond. This previously raised an error; a warning is now given instead, since it is generally not recommended. This makes it possible to cut at a branch point, e.g. keeping only R-CH of R-CH(CH3)NH-R' in the QM region.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]LICENSEfile: [y]