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

[Ruth Helena Tichauer]

Dear Ben,

Thank you for your answer. 

I have no reason to use Slater-Kirkwood parameters rather than other ones, I just wish to use the same for all the sorts of atoms there are in my system and, the way I’ve understood, the ones in the DISPERSION.INP_ONCHSP file match the Slater-Kirkwood ones. 

I’ve first asked about these dispersion parameters for Mg ion on the amber mailing list, but I didn’t get any answers. As dftb has been implemented in Amber, I was hoping to get some enlightenment on this issue or on how to get the dispersion parameters for Mg2+ ion in the same format that the ones for O, N, C, H, S, P are in the DISPERSION.INP_ONCHSP file.

Thank you for any further suggestion,

Sincerely,

Ruth

> On 01 Dec 2016, at 12:35, Ben Hourahine <benjamin.hourahine at strath.ac.uk> wrote:
> 
> Dear Ruth,
> 
> is there any particular reason for the use of Slater-Kirkwood parameters
> for dispersion instead of another model?
> 
> The amber community might be able to help with missing Mg parameters,
> but there are some old papers which give some values fitted against
> experiment, for example
> 
> dx.doi.org/10.1039/TF9696500251
> 
> Regards
> 
> Ben
> 
> On 29/11/16 12:02, Ruth Helena Tichauer wrote:
>> 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,
>> 
>> Sincerely,
>> 
>> Ruth
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> 
> -- 
>      Dr. B. Hourahine, SUPA, Department of Physics,
>    University of Strathclyde, John Anderson Building,
>            107 Rottenrow, Glasgow G4 0NG, UK.
>    +44 141 548 2325, benjamin.hourahine at strath.ac.uk
> 
> 2013/14 THE Awards Entrepreneurial University of the Year
>      2012/13 THE Awards UK University of the Year
> 
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