Re: [AMBER] restraints in igb simulation

From: Danny Xu <quantum_mania.yahoo.com>
Date: Fri, 17 Feb 2012 15:44:32 -0800 (PST)

Typo, how to constrain a ligand to move within a box in igb simulations.



________________________________
 From: Danny Xu <quantum_mania.yahoo.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Friday, February 17, 2012 4:39 PM
Subject: Re: [AMBER] restraints in igb simulation
 
I just wanted to constrain the receptor so that it does not move from its initial position and also constrain a ligand so that it only moves with a box. My question is simply how to achieve this in pmemd when igb is used? Any thoughts are highly appreciated.

-DX



________________________________
From: Jason Swails <jason.swails.gmail.com>
To: Danny Xu <quantum_mania.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, February 17, 2012 5:52 AM
Subject: Re: [AMBER] restraints in igb simulation

It completely depends on what you're trying to do.

Without that it's hard to give anything but the most generic (unhelpful) advice.

Think hard about the question you are trying to answer and what simulation details would be required to probe that.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Feb 17, 2012, at 1:21 AM, Danny Xu <quantum_mania.yahoo.com> wrote:
> Hello,
> 
> In an igb simulation, what would be a good approach to:
> 
> 1. restrain the protein to remove its rotation/translation, in another word, fix its center of mass
> 2. confine a ligand to move only inside a defined 3D box
> 
> Thanks very much in advance!
> 
> -DX
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Received on Fri Feb 17 2012 - 16:00:03 PST