Re: [AMBER] Fwd: Substrate moving out of the box during MD simulation-- reg

From: Jason Swails <>
Date: Mon, 09 Jun 2014 08:24:05 -0400

On Mon, 2014-06-09 at 16:40 +0530, Rajeswari A. wrote:
> Dear all,
> I have simulated an elongated protein in a cubic box (reason being the long
> edges of the protein tilt during simulation and interact with its periodic
> image thus resulting in bad energy values when I had used a cuboid /
> triclinic box ). Now the substrate inside the protein often moves out in
> certain frames during the simulation. Upon visualization, I saw that the
> substrate molecule that moved out, is now becoming a part of its periodic
> image.
> I tried to image using ptraj with following script, but the substrate is
> not imaged back to the protein.
> *trajin md20.dcdcenter :1-476 originimage center origin familiarcenter
> :1-486 mass originimage origin center familiarcenter :1-488 mass
> originimage origin center familiarcenter :1-504 mass originimage origin
> center familiartrajout centered_200.dcd charmm nobox*
> *​Note- *
> 1to 476: protein residues
> 1-486: including one substrate
> 1-488: including second substrate
> 1-504: including protein,substrates and the inhibitor​
> When I do a calculation, especially like binding energy, will the substrate
> be rightly considered in the calculation?
> How can I rectify this, if it is just an imaging problem?
> Kindly give your valuable suggestions in this regard.

Upgrade to the latest version of AmberTools (version 14) and use the
"autoimage" command in cpptraj. It automatically takes care of the
centering, anchoring, and imaging based on the shape of the periodic

For instance:

trajin md20.dcd
trajout centered_200.dcd

(do not put "nobox" unless you strip the solvent and do _not_ want the
periodic box to be saved for future imaging)


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 09 2014 - 05:30:05 PDT
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