Dear Dr. Minehardt,
I have been trying to use your example on the amber website (
http://ambermd.org/Questions/vdw.html) to calculate the rij* and epsilon values for different ion parameters in Amber99.
The procedure works for monovalent ions, but when I compare the numbers you got for Ca2+
r(Ca2+)* = 1.3264 and e(Ca2+)=0.44966
With those in the force field files:
parm99.dat: C0 1.7131 0.459789 Ca2+ Aqvist JPC 1990,94,8021.(adapted)
Then, as you can see, they don't match up exactly and in fact the r* value is very different, even though you also used the A and B values from the referenced article.
When I try your procedure for Magnesium I get:
r(Mg2+)*= 0.7870
e(Mg2+)=0.8750
But again this doesn't match the force field parameters exactly, although I get close:
parm99.dat: MG 0.7926 0.8947 Mg2+ Aqvist JPC 1990,94,8021.(adapted)
The A and B values I have used are taken directly from Aqvist's paper, so I was sure nobody mistyped them somewhere.
Again your procedure works for monvalent ions, i've tried both Li+ and Rb+ just to make sure.
Do you perhaps know why the values for divalent ions values are different?
I have been trying to see if it has something to do with the Lorentz-Berthelot combining/mixing rules, but I don't think so and it don't see why this should only be a problem for divalent ions.
Also the value Ro*=1.768, where does this originate from. I looked in both the Jorgensen and Aqvist papers, but it isn't mentioned explicitly in either of those two.
Best regards,
Jesper
---
Jesper Sørensen, Ph.D.
Postdoctoral Researcher, Amarolab
Department of Chemistry and Biochemistry
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093-0340
http://amarolab.ucsd.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 08 2012 - 22:30:04 PDT
