Hi,
On Friday, May 10, 2013, Andre C. Stiel wrote:
> additionaly info, with ccptraj, i have the problem that he does not want
> to set up my ref:
> > [parm ref.pdb]
> Reading PDB file ref.pdb as topology file.
> > [reference ref.pdb parm]
You specify the parm keyword but not the actual parm. Try 'reference
ref.pdb parm ref.pdb'.
-Dan
> Error: ref.pdb: No frames read. atom=1794 expected 24215.
> Error: Could not set up ref.pdb for reading.
> Error: reference: Could not set up trajectory.
>
>
> On 05/09/2013 09:41 PM, Daniel Roe wrote:
> > 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 <javascript:;>> 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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> >
> >
>
>
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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 Fri May 10 2013 - 06:00:05 PDT
