Re: AMBER: Average structure

From: Thomas Cheatham <>
Date: Thu, 17 May 2007 08:57:12 -0600 (Mountain Daylight Time)

> I am attempting to generate an average structure over so many frames and
> not the total trajectory. I did this in ptraj by the following commands:
> trajin LIP4NWMD4.mdcrd
> average LIP4NWMD4_Avg.pdb start 1 stop 200 pdb
> However, the out put files says that "Coordinate processing will occur
> on 400 frames" and not the 200 frames I attended to indicate in my

All 400 frames will be processed still, but only 1-200 will be used for
the average command; the idea is that you can create multiple average
structures in a single run...

  average LIP4NWMD4_Avg-1-200.pdb start 1 stop 200 pdb
  average LIP4NWMD4_Avg-100-300.pdb start 100 stop 300 pdb
  average LIP4NWMD4_Avg-200-400.pdb start 200 stop 400 pdb

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Received on Sun May 20 2007 - 06:07:22 PDT
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