Make sure masses are copied from termini databases

Masses should always be copied from termini databases,
where they are mandatory since they are specified before
the charge, rather than picking them from atomtypes.atp.
This patch also adjusts a few of the default CHARMM27
charges in atomtypes.atp that deviated in the 3rd decimal.

Fixes #1207.

Change-Id: I6f0c87989ae285ff435cd56c64432988c6634824