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

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Mon, 20 Oct 2014 13:41:44 -0400

Hi Jinfeng,

This question has been answered before by Professor Ross Walker.

Follow this procedure.

http://archive.ambermd.org/200709/0211.html

The same approach is also described for copper ion at
http://ambermd.org/tutorials/advanced/tutorial1_orig/section2.htm

If you want to account for the perturbation of charges around the calcium
ion due to its presence, RESP charges can be derived following the
procedures at http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1

----Sajeewa



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.
>
> Best,
> Jinfeng
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Received on Mon Oct 20 2014 - 11:00:02 PDT