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

[Justin Lemkul]

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

> 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

========================================