Hello Aravind,
Thanks for your interest in our work. You can download the parameter
files from here:
http://www.strodel.info/software.php
If you want to use the parameters from the JMB paper, you can also use
the parameters files above,
but change the parameters accordingly.
If you have any further question, please let me know!
All the best,
Qinghua
On 08/27/2018 07:57 AM, Aravind Ravichandran wrote:
> 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 Mon Aug 27 2018 - 03:00:02 PDT
