Thanks Scott.
That was the problem! I WAS missing something "simple"...ugh.
I am getting the correct data now.
Thanks again, Steve
________________________________
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Scott Pendley
Sent: Wednesday, August 16, 2006 1:20 PM
To: amber.scripps.edu
Subject: Re: AMBER: Ptraj selecting specific atoms in specific residues
Steve,
Have you tried using your first command without a space between ':1-2'
and '.CA,N'?
Scott
On 8/16/06, Steve Seibold < seibold.chemistry.msu.edu
<mailto:seibold.chemistry.msu.edu> > wrote:
Hello
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
following:
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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Received on Sun Aug 20 2006 - 06:07:05 PDT
