Re: [AMBER] Initial configuration of ADP and ion simulation using AMBER.

From: Abhilash J <>
Date: Wed, 13 Jun 2018 22:16:09 +0530


  Thanks for your suggestion.
  I plan on visualizing the structures of ADP with Mg in PDB and try to
decide what conformation is most probable for my system.
  I hope I get a plausible starting complex.


On Wed, Jun 13, 2018 at 1:22 AM Pengfei Li <>

> Hi Abhilash,
> > From your experience what will be the profit of using a hybrid model.
> A hybrid model will only allows the coordination bonds with nonbonded
> model representation move during the simulation. I am not an expert in ATP
> chemistry, you can decide which kind of model to be used for your
> simulations.
> -Pengfei
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Received on Wed Jun 13 2018 - 10:00:02 PDT
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