Re: AMBER: calcium parameter for GB

From: Wei Chen <cwbluesky.gmail.com>
Date: Thu, 18 Jan 2007 11:15:45 -0500

I am really confused about Ca2+ vdw radius. According to Aqvist, it should
be 1.326. But in parm99.dat, it is 1.71. In different paper, different
values were used. I am wondering which one should be the best in general
cases.

Wei


On 1/17/07, Ji-Lai Li <jlutcc.gmail.com> wrote:
>
> Thanks Chen and Zhang!
>
> The electrostatic calculations might affect. But in one of my two
> minimizations with explicit solvent, Ca2+ escapes from its binding pocket as
> well. I think it is more due to the van der Waals radius of Ca2+ ion (atom
> type C0) in parm99.dat. In your case, the explicit solvent might occupy
> the space where Ca2+ previously escaped to, making the escape harder.
>
> The fact is the Ca2+ is stable when igb=0 while Ca2+ will escape when
> igb>0 in my simulation. No steric effects.
>
>
> > These tests and simulations indicate that Aqvist's parameters for Ca2+
> > ions are reasonable and better that the default ones in parm99.dat(derivation of the default values are still unclear). They also seem to
> > indicate that there is no need to form pseudo-bonds between a Ca2+ ion with
> > its coordinated oxygens given the reasonable vdw parameters.
> >
>
> 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.
>
>
>
>
>

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Received on Sun Jan 21 2007 - 06:07:22 PST
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