AMBER Archive (2006)

Subject: RE: AMBER: Ptraj selecting specific atoms in specific residues

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Wed Aug 16 2006 - 12:50:16 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Scott Pendley
Sent: Wednesday, August 16, 2006 1:20 PM
To: amber_at_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_at_chemistry.msu.edu
<mailto:seibold_at_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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