Re: [AMBER] Na cation drifts away from metal chelating protein

From: Elvis Martis <>
Date: Sun, 19 Feb 2017 10:41:16 +0000

You can use ntr = 1 followed by restraint_wt = ?? (high enough to hold the NA ion) and restraintmask = :residue_number_for_that_particular_ion.
And don't forget to define ref = (appropriate reference coordinate file) in your command to submit the production phase.

    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: Michael Shokhen []
Sent: Sunday, February 19, 2017 3:15 PM
Subject: [AMBER] Na cation drifts away from metal chelating protein

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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