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

Justin Lemkul jalemkul at vt.edu
Fri Nov 16 22:49:22 CET 2012

On 11/16/12 4:01 AM, Steven Neumann wrote:
> 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

Thanks for finding this.  I will encourage a citation to be added in the OPLS 
force field about this.

> 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?

It's up to you whether you believe the parameters are reliable enough for 
whatever it is that you're doing.  I can't assess that for you.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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