Ji-Lai Li wrote:
> The fact is the Ca2+ is stable when igb=0 while Ca2+ will escape when igb>0 in my simulation. No > steric effects.
I tried minimizations using igb=0 without explicit solvent as well, and as you observed Ca2+ did not escape. So GB could play a role in the escape of Ca2+, possibly due to the uncalibrated Born radius of Ca2+ as Chen and Case discussed. But igb=0 without explici solvent means a vacuum simulation, which does not seem quite consistent with the van der Waals parameters of Ca2+ derived from solvent environment. Thus, whether the escape of Ca2+ in GB simulations is due to Ca2+'s Born radius for electrostatics or its vdw radius for LJ potential does not look clear at this point. It is clear that Ca2+ ions need be carefully monitored during GB simulations, such as minimizations of initial structures. For molecular dynamics, it will be better to use explicit-solvent simulations, unless the Born radius of Ca2+ is calibrated for GB simulations. So the question again becomes what vdw parameters of Ca2+ should be used in explicit-solvent simulations.
> 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, 3043–3051.
I read the BJ paper, but it looks they use the default vdw parameters of Ca2+ in AMBER. Could you tell me how r=1.6 is derived?
Thanks,
Qing
=========================================
Qing Zhang, Ph.D.
The Scripps Research Institute
10550 North Torrey Pines Road, mail MB-5
La Jolla, CA 92037
858-784-2333 (Lab), 917-509-3182 (Cell)
qzhang.scripps.edu, www.qingzhang.info
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Received on Wed Jan 24 2007 - 06:07:41 PST
