BUG: New amber velocities fix

Fixes the scaling of velocities upon reading/writing Amber restart files. Avoids warnings about netcdf files not being closed properly read_energy now also works for files containing multiple energies Improves testing of amber by writing its own 2h2o.pdb file in an appropriate format Resolves Issue #1505

Checklist

• I am familiar with ASE's contribution guidelines.
• Doc strings in code changed in this MR are up to date.
• Unit tests have been added for new or changed code.
• Issue is resolved via "closes #XXXX" if applicable.