enable selection of Nter and Cter states at topology generation

[VGPReys]

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Checklist

• Tests added for the new code
• Documentation added for the code changes
• Modifications / enhancements are reflected on the haddock3 user-manual
• CHANGELOG.md is updated to incorporate new changes
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

This PR adds two new parameters in the topoaa module enabling the tune the states of Nter and Cter residues.
These parameters are molecule parameters (topoaa.molX), and can be specified for all molecules.

• charged_nter: This option defines how N-terminus residue should be. If false (default), N-ter will be an uncharged NH as it would be in a peptide bond. If true, N-ter will be a charged NH3+. (default false)
• charged_cter: This option defines how N-terminus residue should be. If false (default), C-ter will be an uncharged CO, as it would be in a peptide bond. If true, C-ter will be a charged COO-. (default false)

Related Issue

Closes #1269

Additional Info

Todo:

• add integration tests
• make sure it is functional when self_contained = true
• update user manual