[AMBER] Protein_plus_ADP_plus_Mg2+_preparation_general_rule

From: Antonio Amber Carlesso <antonio.amber.carlesso.gmail.com>
Date: Tue, 19 Feb 2019 19:57:26 +0100

Hi all,

We are interested in performing a MD simulations of a protein where on its
kinase active is co-crystallized ADP and Mg2+

Is there any general rule when we would like to simulate a system with a
divalent cation (in this case Mg2+) in its pocket site?

A simplistic approach could be remove the ion before simulations.

When this "simplistic approach" could be considered a bias in the analysis?

 Any considerations/reflections about it?

Thank you!
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Received on Tue Feb 19 2019 - 11:00:04 PST
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