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when the number of molecules does not agree
with the number of holders.

Don't parse resid, since we don't do anything with it anyway and it is not required to be an integer.

Adding alternative names of terminal nucleic acids (5' and 3' as DG5 and DG3). Adding alternative names of atoms H2', H2'', H5' and H5'' for nucleic acids.

Implemented private _addIons method that improves placement of ions in solvated box, specially for membrane systems

Has a much smaller effect compared to caching the improper search, but non-negligible and easy to do.

This reverts commit 5ef91d22.

* Improve vec3

* Added a ``__neg__`` operator overload so that -Vec3(1, 2, 3) returns
  the same thing as Vec3(-1, -2, -3)
* Derived Vec3 from namedtuple instead of tuple. This allows you to
  access the 3 elements of the vector by name. i.e., vec.x, vec.y, vec.z

* Make sure we use floating point division all the time.

* Implementation of OPLS through DMS reader

* Improved Implementation of OPLS through DMS reader

* raise errors for invalid implicit solvent settings