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

From: Adrian Roitberg <>
Date: Wed, 16 Jan 2019 13:31:42 -0500

you need to image (and maybe center) your trajectory before visualizing it.

Look at the tutorials, and in particular, at the autoimage command in


On 1/16/19 1:29 PM, Amartya Pradhan wrote:
> 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
> *Amartya Pradhan*
> Batch of 2020, Bachelor of Engineering (B.E.)
> Division of Biotechnology,
> Netaji Subhas University of Technology (formerly Netaji Subhas Institute of
> Technology),
> Sector 3, Dwarka, New Delhi-110078, India
> [LinkedIn <>] [ResearchGate
> <>]
> ᐧ
> _______________________________________________
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Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
AMBER mailing list
Received on Wed Jan 16 2019 - 11:00:03 PST
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