> How do I make sure that the water molecules from the original pdb are
> retained during the prmtop and inpcrd file generation?
If you load them in the pdb, they will be retained. If you want to
persuade yourself that this is happening, after you saveamberparm,
use ambpdb to generate a pdb file, edit out all the waters after
the number retained, and view the pdb.
Bill
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Received on Tue Jun 15 2010 - 10:00:04 PDT
