On Tue, Sep 11, 2012 at 2:07 PM, Sasha Buzko <obuzko.ucla.edu> wrote:
> Jonathan,
> the syntax for addions command is as follows: addions <model_name> <ion>
> <number of ions>
> The last argument is the number of ions you wish to add, not the desired
> total charge.
>
> In your case, the command will be: addions pdb Na+ 3
>
If you use "addions pdb Na+ 0", it will add as many ions as necessary to
neutralize the system (or print out an error of the net charge is already
positive). 0 is a special case, however. Any positive number will add
that many ions (so in this case, 'addions pdb Na+ 0' and 'addions pdb Na+
3' have the same effect).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Sep 11 2012 - 12:00:04 PDT
