wrote:
I'm modleing a complex with a copper ion Cu(1). I searched for copper paramters in the modlib/restyp.lib but I did not find them. Are topology and suitable forcefield parameters available?
You're probably best off using a BLK residue ('.') for metal ions. They are just treated as points anyway in MM forcefields, so while you could conceivably obtain parameters from the CHARMM forcefield guys (e.g. www.charmm.org) all you'd be getting would be a charge and a van der Waals radius (and Modeller does not use electrostatics by default in any case).
You are probably more interested in getting the coordination sphere correct, and that generally requires additional scoring terms. automodel will automatically add distance restraints to try and maintain the coordination present in your template (see http://salilab.org/modeller/9v2/manual/node67.html) or you can add your own restraints.
Ben Webb, Modeller Caretaker
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