Re: [AMBER] restrain protein with two different force constant

From: Elvis Martis <>
Date: Tue, 10 Jan 2017 15:11:26 +0000

I don't think this can be done automatically, since sander or pmemd will never know how you want to it.
You can run your simulations in several cycles, where the output of previous cycles serves input for next cycle.
At every cycle you can reduce the restraints by whatever value you wish to and your last cycle can be a without any restraints.
I hope this is what you want to do.

    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: Khabiri, Morteza []
Sent: Tuesday, January 10, 2017 8:29 PM
Subject: [AMBER] restrain protein with two different force constant


I have a protein with two domain. One domain exist in crystal structure but the other one is modeled.

In order to have a right conformation I would like to make both domains restrains but release the restrain gradually from the modeled domain. I don't see any option in amber documentation to do it automatically.

Is there any suggestion how can I set amber config file based on this plan?


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