AMBER Archive (2007)

Subject: AMBER: Average structure

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Thu May 17 2007 - 09:33:41 CDT

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

 

go

 

 

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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