AMBER Archive (2005)

Subject: AMBER: Calculate vdw parameters for alkaline earth metal ions

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Fri Apr 22 2005 - 17:19:23 CDT

Amber lovers:

Our group needs the vdw parameters for strontium ion, so we studied
how ion parameters were calculated in parm99.dat from the Aqvist paper
(JPC 1990,94,8021). According to that paper, the vdw paramters,
epsilon_I and R_I, can be obtained by following equilations:

A_I * A_O = ((epsilon_I * epsilon_O)^0.5) * (( R_I+R_O)^12)
B_I * B_O = 2*((epsilon_I * epsilon_O)^0.5) * (( R_I+R_O)^6)

where A_I and B_I are from Aqvist paper table I and II, A_O = 763.5
and B_O = 24.4 for TIP3P water, epsilon_O=0.1520 and R_O = 1.7683
from parm99.dat.

Our results are as follows
Li 1.1373010 0.0182806
Na 1.8679974 0.0027724
K 2.6579446 0.0003277
Rb 2.9560805 0.0001705
Cs 3.3954300 0.0000806
Mg 0.7868786 0.8751198
Ca 1.3262654 0.4496963
Sr 1.7414584 0.1182361
Ba 2.1243656 0.0471005

And the parameters from parm99.dat are:
  Li 1.1370 0.0183 Li+ Aqvist JPC 1990,94,8021. (adapted)
  Na 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted)
  K 2.6580 0.000328 K+ Aqvist JPC 1990,94,8021. (adapted)
  Rb 2.9560 0.00017 Rb+ Aqvist JPC 1990,94,8021. (adapted)
  Cs 3.3950 0.0000806 Cs+ Aqvist JPC 1990,94,8021. (adapted)
  MG 0.7926 0.8947 Mg2+ Aqvist JPC 1990,94,8021.(adapted)
  C0 1.7131 0.459789 Ca2+ Aqvist JPC 1990,94,8021.(adapted)

For alkali metal ions, our calculation results give the same value as
the parameters from parm99.dat. However, for magnesium, our numbers
are not very close to parm99, and for calcium, our numbers and parm99
are quite different. We have checked the archives of amber mail
reflector and found Dr. Cailliez found the same problem one year
before (http://structbio.vanderbilt.edu/archives/amber-archive/2004/3977.phtml),
but it seems no one explained why this happened. Are there any other
optimizations are used in developing Ca++ and Mg++ parameters? If so,
what should we do if we want to calculate the parameters for strontium
ion?

Thanks
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