Hi there!
I'm just working on something similar, and run into problems with MCPB (basically, it recognizes calcium (Ca) as C-alpha carbons (CA)). As per Pengfei's suggestions, I've been trying the non-bonded model using the compromise ions frcmod for TIP3P waters, and it's working wonderfully. You just need to generate a library based on those parameters, since apparently there is no default calcium residue. Then, just change the name of your calcium to comply with your library, and run tleap using the ion frcmod of your choice, and you're good to go.
All the best,
Manuel
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Received on Mon Oct 20 2014 - 16:30:02 PDT
