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 - 11:00:02 PDT
