James,
The charge of the unit is 0.999040 which is fairly close to 1.0. This warning is useful for checking your units total charge because it may indicate missing atoms or incorrect unit topology. Check that all the atoms are present and that the bonding is correct in that unit.
I think it should be fairly easy to search for atoms within a certain range of Z coordinates. Probably VMD or PyMOL can do this. Or it could be scripted in BASH or Python as well. Once you know which molecules need to be deleted, then it's just a matter of writing a script to remove the molecules from your input structure file.
All the best,
Ben Madej
UCSD Chemistry and Biochemistry
SDSC
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Received on Wed Jun 11 2014 - 14:00:02 PDT
