AMBER Archive (2004)

Subject: AMBER: average structure using ptraj

From: NI AI (aini_at_UMDNJ.EDU)
Date: Thu Jul 01 2004 - 11:18:34 CDT

Dear Ambers,

  I tried to use ptraj in AMBER7 to average the last 200 frame of my MD run.
The script I used:

traj << EOF
trajin AR.md7.crd 300 500
center :1-250
image center familiar
average average.rst restrt

Then I did one more miminization for 5000 steps. It didn't go through.
The EEL term became ********.
Anyone has ideas of what might go wrong?


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