Re: [AMBER] How can I get amber know calcium

From: Jason Swails <>
Date: Mon, 20 Oct 2014 13:44:23 -0400

On Mon, Oct 20, 2014 at 12:35 PM, jinfeng liu <>

> 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?


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Oct 20 2014 - 11:00:02 PDT
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