On Tue, Sep 11, 2012, Jonathan Gough wrote:
>
> addions am1 Na+ 0
> Na+ has a charge of 0.
> addIons: Can't neutralize.
The second line above is the problem: we need to know what version of
AmberTools you are using and (more to the point) what leaprc file(s) you
loaded.
You can see details about what is going on yourself: typing "list" at the
prompt will give you details about what units are loaded. The "desc" command
will give details about each unit:
desc Na+.1.Na+
should give info about what charge LEaP thinks Na+ has. I guessing the
problem is in what force field files you loaded (or didn't load).
....dac
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Received on Tue Sep 11 2012 - 17:30:04 PDT
