[gmx-users] CU2+ nonbonded parameteres (sigma and epsilon)

[Justin Lemkul]

On 3/16/19 9:06 AM, Mohsen Asadbegi wrote:
> Thanks for your answer,
>
> I want to simulate interaction of amyloid-beta peptide and CU(II) ion in
> non-bonded modes. Non-bonded parameters of some metal ions like ZN(II),
> CAD(II), and CA(II) are provided in CHARMM36. So what is the difference
> among copper ion and zinc/cadmium and calcium ions? Moreover, I the last
> version of CHARMM36, non-bonded parameters of the copper metal CU is added,
> but I need parameters of the CU(II) ion.

Pairwise-additive force fields do not treat transition metals well. 
There are some approximate parameter sets, including a full set of 
parameters that are purportedly compatible with CHARMM (e.g. 
dx.doi.org/10.1021/jp309150r) but they do require additional refinement 
in the context of protein interactions.

In short, trying to derive any useful information in terms of ion 
comparisons in systems like these is beyond the current capabilities of 
classical, nonpolarizable MD simulations. QM/MM is the way to go (and 
there are numerous studies already published that have done what you're 
seeking to do). As Paul said, there are physical properties that MD 
force fields cannot describe, which have profound impact on the 
properties that are critical to the comparison you seek to do, not the 
least of which would be charge transfer and coordination geometry. A 
sphere with +2 charge will never get those things right.

-Justin

> Regards
> Mohsen
>
> On Sat, 16 Mar 2019 at 16:28, Paul Bauer <paul.bauer.q at gmail.com> wrote:
>
>> Hello,
>>
>> Classical force fields are a bad way to describe the behaviour of
>> transition metals such as CU2+, because they are not able to cover the
>> behaviour of the D-orbitals with just the sigma and epsilon parameters.
>> What are you planning to use the model for? It is possible to parametrize
>> transition metals for this, but it is a lengthy and time consuming process.
>>
>> Kindest regards
>> Paul
>>
>> On Fri, 15 Mar 2019, 19:53 Mohsen Asadbegi, <mohsenasad.7091 at gmail.com>
>> wrote:
>>
>>> Hi!
>>>
>>> I need to add non-bonded CU2+ ion to CHRAMM36. How can I find these
>>> parameters (sigma and epsilon)? Does it enough to define CU2+ by its
>>> charge, mass, sigma and epsilon?
>>> In addition, I want to know that what are the units of sigma and epsilon
>> in
>>> the CHARMM36 force field?
>>>
>>> Regards,
>>> Mohsen Asadbegi.
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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