[gmx-users] Fe(2+) nonbonded parameters
jalemkul at vt.edu
Thu Nov 15 18:51:12 CET 2012
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.
> 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
>>> ; These ion atomtypes are NOT part of OPLS, but since they are
>>> ; needed for some proteins or tutorial Argon simulations we have added
>>> Cu2+ Cu2+ 29 63.54600 2.000 A 2.08470e-01
>>> Fe2+ Fe2+ 26 55.84700 2.000 A 2.59400e-01
>>> Zn2+ Zn2+ 30 65.37000 2.000 A 1.95200e-01
>>> Ar Ar 18 39.94800 0.000 A 3.41000e-01
>>> 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 A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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