Re: AMBER: calcium parameter for GB

From: Ji-Lai Li <jlutcc.gmail.com>
Date: Wed, 17 Jan 2007 17:25:20 -0800

  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 - 06:07:13 PST
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