Dear Gromacs Users, I am trying to simulate a modeled protein -ligand complex in lipid bilayer using Gromacs 4.5.4 with Charmm27 FF. For my project purpose which is to see the effect of substitution of ions (Ca instead of Na ions) in the protein structure on protein ligand interactions , I have modeled the protein with Ca ions in the protein instead of Na ions. For the same, I was wondering if Gromacs 4.5.4 with Charmm27 FF can simulate Ca ions if incorporated in the protein instead of Na ions as i described here.
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