Fix issue #179

[lohedges]

This PR closes #179 by using continue to skip atoms that aren't in the perturbation template, i.e. those atoms which don't change their charge, LJ, or ambertype properties between the reference and perturbed state.

• I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
• I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y]
• I confirm that I have permission to release this code under the GPL3 license: [y]

Suggested reviewers:

@chryswoods