Re: [AMBER] G quadruplex ions minimization

From: Juraj Dobias <>
Date: Fri, 4 Dec 2020 12:48:33 +0100


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.


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 - 04:00:02 PST
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