Hi,
One of the strengths of cpptraj is that it allows you to specify
multiple topologies, as well as different target and reference masks
to the rms command - the only requirement is that the # of atoms and
their ordering are the same. For example, the input may be something
like (assuming :63-65.CA,C,N is your target mask and
:94,146,220.CA,C,N is your reference mask):
parm ref_structure.pdb [p_ref] # This loads ref_structure.pdb as a
topology tagged [p_ref]
reference ref_structure.pdb parm [p_ref] # This loads the coordinates
from ref_structure.pdb as the reference
trajin prorun_reimaged.mdcrd
rms reference :63-65.CA,C,N :94,146,220.CA,C,N out results.dat
On Thu, May 9, 2013 at 11:02 AM, Andre C. Stiel
<andre.stiel.tuebingen.mpg.de> wrote:
> 2) the rmsd results are absolutely bogus. It looks like in the first
> step where I did NOT specified "nofit" he
> did no fitting or he didnt translate the frame.... I always figured
> ptraj would translate the frame if no "nofit" is specified
No, in ptraj and cpptraj 'nofit' means straight RMSD, do not modify
the coordinates in any way. In cpptraj you can get RMS results with
translation and without rotation by specifying the 'norotate' keyword.
Hope this helps,
-Dan
> In short: I want to first superimpose a set of relatively fixed atoms
> and then measure the rmsd w/o fitting of my moving atoms.
>
> Maybe somebody can help me out.
> Thanks a lot
>
> André
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu May 09 2013 - 13:00:02 PDT
