Re: [AMBER] Abrupt peaks in the RMSD plot of heating trajectory

From: ABEL Stephane <>
Date: Wed, 16 Jan 2019 18:40:05 +0000


You obtain this sort of plot because some part of the protein-ligand cross the box. So you have to center the protein in the simulation box before to compute the RMSD.


De : Amartya Pradhan []
Envoyé : mercredi 16 janvier 2019 19:29
À :
Objet : [AMBER] Abrupt peaks in the RMSD plot of heating trajectory

Dear all,

After heating the protein-ligand complex using AMBER, I have generated the
RMSD plot of the heating trajectory using UCSF Chimera. There are abrupt
peaks in the RMSD plot generated (graph attached). Moreover, while
visualizing the trajectory in Chimera, the ligand can be seen moving out of
the binding pocket for one or two frames and after that, moving back into
the binding pocket.

Kindly suggest me a way to sort this out.

With best regards,
*Amartya Pradhan*
Batch of 2020, Bachelor of Engineering (B.E.)
Division of Biotechnology,
Netaji Subhas University of Technology (formerly Netaji Subhas Institute of
Sector 3, Dwarka, New Delhi-110078, India
[LinkedIn <>] [ResearchGate

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Received on Wed Jan 16 2019 - 11:00:03 PST
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