Which MG parameters (and water)? The recent 12-6-4 may be worth trying if
you have not already. See papers from the Merz group and York group. Look
here: https://ambermd.org/AmberModels_ions.php
On Wed, Mar 16, 2022, 11:46 AM liu kai <kailiu.outlook.com> wrote:
> Dear All,
>
> Recently, I run a simulation of kinase (for PDB:4EOQ as an example)
> containing ATP coordinating with one Mg2+ ion.
> I use antechamber to build the prep file for ATP without any preblem.
> Antechamber -I ATP.mol2 -fi mol2 -o ATP.prep -fo prep -c bcc -n -4
>
> I build the amber file for the complex by adding 6 Na+ as counter ions
> solvated in a TIP3P water box.
> The initial structure of ATP-Mg adapts C3 type, which three O atoms
> coordinate with Mg2+. defined in 10.1021/acs.jctc.0c01205
> After few ns production run, I found two Na+ ions close (about 2.5
> Angstrom) to the phosphate group, except the Mg2+.
> I think the Na+ should not be close to the phosphate group.
> If the simulation is correct, does it mean that ATP can coordinate with
> two Mg2+ ions at the same time?
> but why only one Mg2+ was found in many PDB files?
>
> At the beginning, I think the problem maybe the initial position of Na+
> is not good accidentally.
> So I use below command to keep the Na+ connter ion away from the
> protein, and visually comfirmed.
> addIonsRand xx Na+ 0 3.0
> But after few ns simulation, two Na+ again approach to the phosphate
> group.
>
> Is there any suggestion? Thanks in advance.
>
> Yours sincerely,
> Kai
>
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Received on Wed Mar 16 2022 - 09:00:03 PDT
