The pdb that tleap generates for system that big might be corrupted (the system has probably more than a half million atoms). What you want is to generate the topology and crd file and use those for visualization and simulation.
best,
George
PS: I second Dave on adding the cations after the water box, it will save you few good Angstroms in box length for a system that is already huge.
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Received on Thu Apr 13 2017 - 10:00:05 PDT
