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Adjust pdb2gmx vsite generation for 3 atom site

Paul Bauer requested to merge 4573-fix-vsite-generation-for-tetrahedral-secondary-amines into release-2022

The vsite code wouldn't account for geometry for 3site construction in pdb2gmx and thus wouldn't create the correct tetrahedral structure for things such as secondary amines, and would make them incorrectly planar.

Fixed to include a geometry check.

Fixes #4573 (closed)

Closes #4573 (closed)

Edited by Berk Hess

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