rmcgibbo/mdtraj — pull request #431 by swails (2014-05-01 17:03:43+00:00)
Title: Fix Amber mdcrd parser

The existing mdcrd parser relied on whitespace-delimited fields. In general this is a bad assumption since any atom that moves over 100 Angstroms in the -x, -y, or -z directions will create a number whose `8.3F` width is 8 characters, so there will be no space between that number and the one preceding it. That kills the existing parser, despite the fact that it is a legal (and rather common) ASCII mdcrd file.

Amber does not wrap particles back into the central box by default, so having, for instance, solvent diffuse more than 100 Angstroms in a particular direction is inevitable for a long simulation and doesn't take that much time.

This also fixes a couple typos in the error messages.