AMBER Archive (2006)

Subject: AMBER: Ptraj selecting specific atoms in specific residues

From: Steve Seibold (
Date: Wed Aug 16 2006 - 12:05:16 CDT


I hope I am not missing something simple, but I do have a simple
question concerning the use of "ptraj". I am trying to get rms and
atomicfluc values for specific "atoms" in specific "residues". For
example, let say I have a protein that is 200 residues and I want to
find the rms of CA of only the first two residues. I tried the


rms mass out file.txt time 5 :1-2 @CA,N


atomicfluc out file.txt @CA,N :1-2


Neither of these commands seems to work. I do get data but it is NOT the
data I am searching for. In the first case I get all atoms of residues 1
and 2. In the second case I get atoms CA and N of the whole protein.


Am I doing something wrong or does AMBER not do this?


Thanks, Steve


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