Re: AMBER: Simulating proteins with calcium ion

From: (wrong string) 张勇 <>
Date: Sat, 23 Dec 2006 09:02:57 +0800

In my EF-PROTEIN system, the Ca2+ coordination hold a good octahedron coordination
if we regard the water molecule as a ligand when using the calcium parameter in
amber99 forcefield.

of cource, I change both the radius and the epsilon values to use the small
parameter, calcium ions escape from a C2-domain, but is ok in EF-protein, while
the Ca-O distance is too samll, only 2.1-2.4.

Did I make it clear?

>> ----- Original Message ---> From: <>
>> To:
>> Sent: Tuesday, December 12, 2006 4:25:03 P> Subject: Re: AMBER: Simulating
proteins with calcium i>
> > Hi> I am performing the MD simulation about calcium-binding protein. In >
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>
distance is 2.4-2.7, a little bigger than experimental value 2.2-2.6.
> What does Ca2+ coordination looks like in your syste
> > 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 esca> its binding
site druing the MD in the C2 domain protei
> Did you change the radius alone or both the radius and the epsilon values? Could
you explain why it escaped with a smaller radiu
> > 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
> 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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Received on Sun Dec 24 2006 - 06:07:45 PST
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