Hello!
I would also like to recommend the article:
"Empirical Force Fields for Biologically Active Divalent Metal Cations in
Water"
C. Satheesan Babu and Carmay Lim
J. Phys. Chem. A. 2006, 110, 691-699
Here, you can find the non-bond parameters (vdW) for 25 divalent metal ions
and the exact methodology. They include Cu++ and Mg++.
Hope it helps!
Have a good day!
Rodrigo
2011/7/16 Marek Maly <marek.maly.ujep.cz>
> Hello,
>
> I am also interested about Cu++ Vdw parameters compatible with Amber ff.
>
> I already checked source suggested by Rodrigo ("T Hermann and H Heumann,
> RNA 1995 1: 1009-1017")
> and I unfortunately didn't find any sentence about how they derived these
> parameters.
> Moreover I also noticed that they used parameters for Mg++ r_Vdw = 1.17 A
> and epsilon = 0.1 kcal/mol
> claiming here that these data are from Aqvist JPC 1990,94,8021 although
> after my recalculation of Mg++
> parameters from this work I have obtained r_Vdw = cca 0.923 A and epsilon =
> cca 0.875 kcal/mol (see attached file). Values
> from parm99.dat are r_Vdw = 0.7926 A and epsilon = 0.8947 kcal/mol. In
> parm99.dat there is notice
> (Mg2+ Aqvist JPC 1990,94,8021.(adapted)) which is obvious here but in case
> of "T Hermann and H Heumann, RNA 1995 1: 1009-1017"
> there is almost 9 x smaller well depth (epsilon) than in case of Aqvist.
> This of course may put some doubts also
> to reported Cu++ parameters especially if they do not clearly explain how
> they derived them or from which another
> work they adopted them (so that one could check in the original work that
> data was adopted in the right way).
>
> I attached my transformation of AI and BI Vdw parameters into Amber parm
> format r_vdw and epsilon (well depth).
>
> Any comments welcomed !
>
> Best wishes,
>
> Marek
>
>
>
>
>
>
> Dne Sat, 16 Jul 2011 03:58:06 +0200 ros <rodrigogalindo.gmail.com>
> napsal/-a:
>
>
> Hello!
>>
>> You can use the parameters used by Hermann, T and Heumann, H. RNA,
>> 1995, 1, 1009-1017
>>
>> r_{vdW}=0.96
>> \epsilon=0.01
>>
>> I used those parameters for copper complexes and work acording to
>> X-ray observations. Remember to check you simulated copper structure
>> with some experimental data.
>>
>> Good luck!
>> Rodrigo.
>>
>>
>> 2011/7/15, caobb0214 <caobb0214.163.com>:
>>
>>> Dear Sir,
>>> There is a Cu2+in my molecule and I need its nonbond parameter (van der
>>> Waals radius and well depth) in amber 9. can anyone help
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>>>
>>>
>>
>
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Received on Sat Jul 16 2011 - 16:00:02 PDT
