Re: AMBER: calcium parameter for GB

From: Ji-Lai Li <>
Date: Tue, 23 Jan 2007 18:07:21 -0800

Dear Qing:

> > My simulations run fine when the vdW parameter for Ca2+ ions wsa set
> to r=1.600 and the charge > intact. The Aqvist's parameters can not
> reproduce the NMR structure. The distances between Ca2+ > and its
> coordinated oxygens are 2.4~2.7, which is somewhat longer. I think the r=
> 1.600
> > is also reasonable. Please read Biophysical J V90, 2006, 30433051.
> I read the BJ paper, but it looks they use the default vdw parameters of
> Ca2+ in AMBER.

  I think the paragraph may help you:
The MD simulations were performed for this loop III of CaM (Fig. 1) and
a Ca21 atom, with explicit water solvents using the AMBER 7 program (24),
in which the parm99 force field for protein atoms (25), the parameters of
Bradbrook et. al. (26) for Ca2+, and the TIP3P potential for water molecules
(27) were used.

where ref. 26 is J. Chem. Soc. Faraday T. 94:16031611. In this ref. it
For the non-bonded parameters of Ca2` and
Mn2`, a well depth of [0.014 kcal mol~1,40 and van der
Waals radii of 1.79 A and 1.69 A, respectively, were used.

>Could you tell me how r=1.6 is derived.

As J. Chem. Soc. Faraday T. 94:16031611. indicates, the r=1.600 was chosen
to maintain reasonable geometry
around the metal centres during energy minimisation of the EF-hand. My
simulations with r=1.367, 1.7131, 1.50, 1.55 and 1.60 indicate the later (r=
1.60) is the best value.
I am not sure whether the value is accurate, but no other choice for me now.

I am looking for further discussions.

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Received on Wed Jan 24 2007 - 06:07:45 PST
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