AMBER Archive (2009)

Subject: [AMBER] essential dynamics

From: Chunliyan (chunliyan_at_mail.utexas.edu)
Date: Wed May 13 2009 - 11:23:23 CDT

Hi, all

         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.

  

All the best,

-Chunli
chunliyan_at_mail.utexas.edu
<chunliyan_at_mail.utexas.edu">http://cn.mc150.mail.yahoo.com/mc/compose?to=chunliyan_at_mail.utexas.edu> or
chunliyan_at_yahoo.com.cn
<chunliyan_at_yahoo.com.cn">http://cn.mc150.mail.yahoo.com/mc/compose?to=chunliyan_at_yahoo.com.cn>

 


  • application/octet-stream attachment: PCA.rar

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