AMBER Archive (2006)

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

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Wed Aug 16 2006 - 12:32:24 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
> 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.

There is a command in "rdparm" called checkmask that is useful for
debugging your atom selection. It may be choking on the space, as pointed
out by Pendley (yes, I just checked this).

  rdparm prmtop
  checkmask :1-2 @CA,N

Note that you are wise to do the RMS fit prior to doing the atomicfluct.
Better would be to fit to the average structure (loading an average
structure as a reference and then doing rms reference), but the rms to the
first frame (as above) is probably reasonable.

Note also that if you are using AMBER 9, that ptraj version have an
additional parser that recognizes quotes, | and & so that you could try

 ":1-2 @CA,N"

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