AMBER Archive (2006)

Subject: AMBER: average struct.problem

From: bala (cbala_at_igib.res.in)
Date: Thu Jun 22 2006 - 04:11:15 CDT

hi amber users,
 
i have simulated a 12mer DNA with water and ion. After dynamics i did imaging of the trajectory file and saved is as a new file. i hv given the script below.
 
trajin at_traj.mdcrd
trajout at_imgd.mdcrd
center :1-24 mass origin
image origin center
center:1-5223 mass origin
image origin center familiar
go
 
now when i calculate the average structure from this imaged trajectory, all water molecules and ion cluster around the center of DNA. I have gone through the previous mails on this issue but i am not get whether the problem can be fixed. someone kindly help me on this.
 
thanks in advance,
c.bala

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