Dear people of the Amber community,
I have a question about running an NMR refinment on a nucleic acid - silver system. In the system I have silver ions bound within DNA base pairs in place of some of the usual hydrogens. What is a sensible approach to this problem? Can I define new, deprotonated residues and make a non-nonded model, or should a bonded model be used? In the latter case, are appropriate parameters for the silver ion in this environment already available somewhere, or do I have to develop new parameters?
Best regards,
Uroš
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Received on Fri Apr 12 2019 - 06:30:06 PDT
