(wrong string) Ⅱ) ion

From: Marek Maly <marek.maly.ujep.cz>
Date: Sun, 17 Jul 2011 01:56:24 +0200

Hi Rodrigo,

thanks a lot for this nice and relatively fresh article !
It seems, that they were inspired by Aqvist a little but instead of
using absolute hydration energies they used differences in hydration
energy between studied ions and reference one (here Zn) etc. (I will read
in detail later)

I compared their data with that 3 divalent cations already present in
parm99.dat file (Mg++, Ca++, Zn++) and
unfortunately I found relatively huge differences in well depths
(epsilons) - see below (in each case first line is from parm99, the second
line from
  "C. Satheesan Babu and Carmay Lim J. Phys. Chem. A. 2006, 110, 691-699"

             r_Vdw epsilon
MG 0.7926 0.8947 Mg2+ Aqvist JPC
1990,94,8021.(adapted)
Mg2+ 1.1826 0.0620

C0 1.7131 0.459789 Ca2+ Aqvist JPC
1990,94,8021.(adapted)
Ca2+ 1.8311 0.0278


Zn 1.10 0.0125 Zn2+, Merz,PAK, JACS,113,8262,(1991)
Zn2+ 0.8800 0.1830



However there is also this sentence in "C. Satheesan Babu and Carmay Lim
J. Phys. Chem. A. 2006, 110, 691-699"

"Since the parameters have been developed using the "conventional" PEF,
they can be easily integrated with
the widely used biomolecular force fields such as CHARMM or AMBER". which
seems to be in disagreement with
above reported comparison.

So to be frank I don't know now which parameters are more trustworthy for
Amber calculations. On one side I would like to believe
that "C. Satheesan Babu and Carmay Lim J. Phys. Chem. A. 2006, 110,
691-699" provides more accurate values then that already
present in parm99.dat file (adopted from cca 20 years old works) but in
this case I don't understand why that old parameters
was not already actualized. There has to be some reason why this old
values are still maintained in parm99.dat file. Just
to maintain compatibility of actual works with old simulation results
which included these ions ?

Any comments welcomed !

   Best wishes,

      Marek









Dne Sun, 17 Jul 2011 00:35:56 +0200 ros <rodrigogalindo.gmail.com>
napsal/-a:

> 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 - 17:30:02 PDT
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