[DFTB-Plus-User] Dispersion parameters for Mg2+ ion

Ruth Helena Tichauer rhtichau at laas.fr
Tue Nov 29 13:02:01 CET 2016

Dear DFTB community,

I’m trying to run a QM/MM simulation of a protein and its ligand using amber package. I wish to use the dftb parameters for the QM region, using the dispersion correction parameters within the DISPERSION.INP_ONCHSP file that looks like:

O 0.560 0.560 0.000 0.000 3.8 3.8 3.8 3.8 3.15
N 1.03  1.03  1.090 1.090 3.8 3.8 3.8 3.8 2.82
C 1.382 1.382 1.382 1.064 3.8 3.8 3.8 3.8 2.5
H 0.386 0.386 0.000 0.000 3.5 3.5 3.5 3.5 0.8
P 1.6   1.6   1.6   1.6   4.7 4.7 4.7 4.7 4.5    !PO4
S 3.0   3.0   3.0   3.0   4.7 4.7 4.7 4.7 4.8    !S not SO2 

As I have a Mg2+ ion, my calculation within amber fails with the following error message:
“Dispersion parameters for atom Mg not found”

Although Mg2+ is a cation and so it’s electronic cloud might be only slightly polarizable, I wonder if Slater-Kirkwood parameters have been calculated in order to add them to the dispersion parameters file and be able to run the simulation. If they haven’t, are there any values that you could suggest or a protocol to follow to obtain them? I’ve also been looking for articles on this matter and I’ve found several but I’m not experienced enough to “choose” a set (even if I haven’t really found one that matches the format of those in the DISPERSION.INP_ONCHSP file) and I don’t want to take the risk and accidentally use those that actually are for Mg, whose dispersion is probably completely different from the dispersion of Mg2+.

Thank you a lot for any information/suggestion/paper on this matter,



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