For quadruplexes and ions, we have published recently
some benchmark AMBER MD simulation studies, with different ion parameters
and water models:
https://pubs.acs.org/doi/10.1021/acs.jctc.9b01068
and
https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00257
Regarding placing into the NMR structures and model structures:
simply manually into
all inter-tetrad cavities, the simulation will do the rest on
its own, obviously within the force-field approximation.
The approximations are not negligible and the latest review is:
Annual Reports in Medicinal Chemistry
Volume 54, 2020, Pages 197-241
https://www.sciencedirect.com/science/article/pii/S0065774320300154
Best wishes Jiri
On Fri, 4 Dec 2020, Bill Ross wrote:
> Date: Fri, 4 Dec 2020 09:53:49 -0800
> From: Bill Ross <ross.cgl.ucsf.edu>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: amber.ambermd.org
> Subject: Re: [AMBER] G quadruplex ions minimization
>
> Typically one wants to run dynamics after minimization, and that is when
> your ions will be most likely to exit, and if it happens when you think
> it shouldn't, restraints are the answer.
>
> If you haven't seen my old paper on modeling ions in quadruplex, it
> might be worth a look. I wonder if it could be the first, at least with
> amber code?
>
> https://pubs.acs.org/doi/pdf/10.1021/ja00093a003
>
> Bill
>
>
> On 12/4/20 3:48 AM, Juraj Dobias wrote:
>> Hi,
>>
>> I always place them manually. You can do it in pymol for example. Then I
>> do standard minimization in amber with restraint on solute
>> (restraintmask='!(:WAT)&(!(.H))'), so ions are not restrained.
>>
>> You can place them more algoritmicaly by averaging coordinates of H1
>> protons of corresponding 8 guanines.
>>
>> Juraj
>>
>> On 04. 12. 20 0:06, Jisha B wrote:
>>> Dear all,
>>> In certain NMR derived structures of G quadruplexes, there are no ions
>>> present in between the quartets. In such cases, what would be the best
>>> method to add those ions and the minimization protocol to be followed to
>>> ensure that those ions do not move out of the quartets.
>>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
> --
> Phobrain.com
>
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Received on Fri Dec 04 2020 - 11:30:03 PST
