Thanks David,
I will check that.
I was using AmberTools 12, Amber 12 and leaprc.ff12SB
It was curious to me that when I did use the formalism
addions *unit* Na+ 0
that i got the error message Can't neutralize.
on a related note, is it necessary or good/bad form to charge balance a
protein for a minimization and/or basic MD run in explicit or implicit
solvent?
Thanks,
Jonathan
On Tue, Sep 11, 2012 at 8:24 PM, case <case.biomaps.rutgers.edu> wrote:
> 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 Wed Sep 12 2012 - 05:30:03 PDT
