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 - 09:00:02 PDT
