[AMBER] MG Coordination System: Nonbonded Cationic Dummy Model

From: Aravind Ravichandran <raravind.ibab.ac.in>
Date: Mon, 27 Aug 2018 11:27:15 +0530

Dear Amber users,
 I am trying to simulate RNA Polymerase, which contains 2 Mg ions
coordinated with protein, water and incoming nucleotides at the active
site . There is also a coordination bond between these two Mg ions. how
do I model this system?

I went through these papers -
1) J. Phys. Chem. Lett. 2017, 8, 5408-5414
(https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.7b02358).

2)J Mol Biol. 2007 February 16; 366(2): 687–701.
(https://www.sciencedirect.com/science/article/pii/S0022283606015221?via%3Dihub)

I got the parameters from these paper. How do I implement this Non-bonded
cationic dummy model in Amber?

Any help is appreciated !

Thank you in advance,
Aravind R


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Received on Sun Aug 26 2018 - 23:00:02 PDT