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Firstly, I am postign this question to both chemistry and physics stacks exchange as I am not sure to which it belongs and to use the benefits from both sites.
I have modeled missing loops in a PDB structure using chimera. Should I run MD or energy minimization on the output file?
Thank you in advance.
To expand on Mithoron's comment, it's absolutely necessary to equilibrate (or at least minimize the energy) of your system once you've introduced an appreciable perturbation of any sort (in this case, you've appreciably changed the system itself!). To give you an idea, some lesser changes that would still justify equilibration are: changes in solvation, temperature, pressure, protonation of amino acids, oxidation state of cofactors, etc.
Note: by equilibration, I mean letting your system relax in the presence of surroundings. By minimization, I am referring to minimizing the total energy of the protein (explicitly solvated, unless you're doing some odd gas-phase or implicit solvation) in the absence of temperature and pressure (0 K, no thermostat or barostat).
