AMBER Archive (2009)

Subject: Re: [AMBER] essential dynamics

From: David A. Case (
Date: Wed May 13 2009 - 12:15:50 CDT

On Wed, May 13, 2009, Chunliyan wrote:
> I want to perform essential dynamics analysis using IED. I have
> generated the .ppj and .pev file using Ptraj. But when I use IED to
> visualize the results. I found the protein shows abnormal. There are some
> abormal bond between atoms. I don't know why. I want to get a pdb file from
> PCA analysis and then to do domain motion analysis using DYNDOM software.
> How to save a pdb file from PCA. Anyone can help me? The attatched is the
> files I have produced using ptraj and the script I used. Thank you.

Do you get the "abnormal bonds" with a single structure (e.g. from a restart
file)? It's important to find out whether the problems you are seeing are
specific to IED or are more general.


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