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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Received on Fri Dec 04 2020 - 10:00:03 PST
