[gmx-users] Fe(2+) nonbonded parameters

[Steven Neumann]

On Thu, Nov 15, 2012 at 5:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/15/12 12:47 PM, Steven Neumann wrote:
>>
>> So what would you do to get those parameters asap?
>>
>
> Get what parameters?  The ones shown below (except Cu2+) have no citation
> and no one has vouched for their authenticity.  As such, the decision was
> made to delete them to prevent anyone from blindly using them, hoping that
> they are right.  Given this information, it would be unwise to use them
> unless, as I said, you know where they came from and believe them to be
> suitable.
>
> -Justin

I found the source of the Fe(2+) parameters below from QM/MC simulations:

http://www.sciencedirect.com/science/article/pii/S0009261407014388

Please, see table 1. I think it is a reasonable source for the usage
Fe(2+) in aqueous solution with protein.
Would you comment please?


Steven

>
>
>> On Thu, Nov 15, 2012 at 5:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>
>>> On 11/15/12 12:18 PM, Steven Neumann wrote:
>>>>
>>>>
>>>> Dear Gmx Users,
>>>>
>>>> Maybe someone before was simulating Fe(2+) in water and protein system
>>>> using Charmm27 ff. I am looking for nonbonded parametrs. I found in
>>>> OPLSAA:
>>>>
>>>> ; These ion atomtypes are NOT part of OPLS, but since they are
>>>> ; needed for some proteins or tutorial Argon simulations we have added
>>>> them.
>>>>    Cu2+       Cu2+   29  63.54600     2.000       A    2.08470e-01
>>>> 4.76976e+00
>>>>    Fe2+       Fe2+   26  55.84700     2.000       A    2.59400e-01
>>>> 5.43920e-02
>>>>    Zn2+       Zn2+   30  65.37000     2.000       A    1.95200e-01
>>>> 9.78219e-01
>>>>    Ar         Ar     18  39.94800     0.000       A    3.41000e-01
>>>> 2.74580e-02
>>>>
>>>> But not sure whether I can use them?
>>>>
>>>
>>> These are undocumented parameters that are being removed for the next
>>> release. Don't use them unless you can find where they came from and you
>>> trust that source.
>>>
>>> -Justin
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
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>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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