[AMBER] Na cation drifts away from metal chelating protein

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Sun, 19 Feb 2017 09:45:13 +0000

Dear Amber experts,

I have on my Linux server Amber16 and AmberTools16.
I am doing molecular dynamics simulation of protein with ff14SB force field
and explicit TIP3 water solvent. The initial crystal structure of my protein
contains chelating by protein Na cation.
During the production phase MD simulations after 200ns the Na metal cation
is moving to the water solvent far away (about 55 A) from its initial position
inside protein.
What is the command line that should be added to the input file for
the restrained MD simulation to prevent the Na cation drifting away
from its chelating complex in protein?

Thank you,

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Received on Sun Feb 19 2017 - 02:00:02 PST
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