On Thu, Aug 03, 2017, James Starlight wrote:
> The file contained 1 atoms not in residue templates
I'd suggest tracking down the source of this message.
Beyond that, this is not something that can be readily debugged via email.
You report that just removing water molecules changed the net charge of your
system. It seems clear that something else actually changed, but only you
can find out what that is.
Start with a very small protein/peptide (or with just a box of pure water).
Repeat your procedure, in order to generate the simplest example tha exhibits
the behavior you see.
The "summary" command of parmed is a simple way to look at net charges, and
you can print individual atom charges in that program as well.
....dac
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Received on Thu Aug 03 2017 - 05:00:02 PDT
