AMBER Archive (2006)

Subject: Re: AMBER: Simulating proteins with calcium ion

From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Date: Fri Dec 22 2006 - 14:22:53 CST

> ----- Original Message ----
> From: 张勇 <clarkzhy_at_mail.bnu.edu.cn>
> To: amber_at_scripps.edu
> Sent: Tuesday, December 12, 2006 4:25:03 PM
> Subject: Re: AMBER: Simulating proteins with calcium ion
>
> Hi,
> I am performing the MD simulation about calcium-binding protein. In my
> experience, the calcium parameter in parm99.dat of Amber8/9 is a little big. when
> I do periodic boundary condition(PBC) simulation with TIP3P water model,the Ca£­O
> distance is 2.4-2.7, a little bigger than experimental value 2.2-2.6.

What does Ca2+ coordination looks like in your system?

> but ,when I use the parameter posted by Kenley Barrett on AMBER achieve, and
> reduced the radius of Ca2+ to about 1.3. the calcium ions escape
> its binding site druing the MD in the C2 domain protein.

Did you change the radius alone or both the radius and the epsilon values? Could you explain why it escaped with a smaller radius?

 
> so,I think the calcium parameter in parm99.dat is just OK for explicit water
> model, periodic boundary condition(PBC) simulation, through it cause a little
> bigger Ca£­O distance.

So far, I have done minimizations with both implicit solvent (GB used) and explicit solvent (GB not used). In both cases, Ca2+ escapes the binding pocket by more than 1 Angstrom. In the explicit-solvent minimization, the distances between Ca2+ and the 6 oxygens range from 2.74 to 3.52 with an average of 3.10. I have not done MD with PBC yet since mimizations do not look right.

Thanks,

Qing

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