AMBER: Average structure

From: Steve Seibold <>
Date: Thu, 17 May 2007 10:33:41 -0400

Hi Amber


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
commands. Am I misunderstanding what the start and stop is? Should I
just put "trajin LIP4NWMD4.mdcrd 1 200" and delete the start and stop
commands on the other command line?


Thanks, Steve


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