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

From: Rajeswari A. <rajeswari.biotech.gmail.com>
Date: Mon, 9 Jun 2014 16:40:35 +0530

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

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.

​thank you in advance.​

M.S. Research Scholar
Computational Biophysics Lab
Department of Biotechnology
Indian Institute Of Technology, Madras
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Received on Mon Jun 09 2014 - 04:30:02 PDT
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