It is a free ion. Ok, I have read the amber manual for that. Thank you all.
2014-10-20 10:44 GMT-07:00 Jason Swails <jason.swails.gmail.com>:
> On Mon, Oct 20, 2014 at 12:35 PM, jinfeng liu <jinfengliu1119.gmail.com>
> wrote:
>
> > Dear Amber users,
> >
> > I want to run MD simulation for a protein which contains a calcium. I
> know
> > the parameters of calcium are included in amber. So, what should I do to
> > get amber know the calcium in the pdb. Thank you.
> >
>
> Please describe better what you are trying to do. Is it a bound calcium?
> Do you want to model it using covalent bonds to various residues in your
> protein? Do you just want it as a free ion (if so, see chapter 3 section
> 9)? What have you tried so far? Did it not work? How did it fail?
>
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Oct 20 2014 - 11:00:03 PDT
