Hi,
The [p_ref] was part of something you can do in cpptraj with topologies and
ref coords called tagging, which essentially allows you to refer to them by
an alias (instead of the file name which may be very long). There are some
examples in the manual.
Let me know if you have further questions.
-Dan
On Friday, May 10, 2013, Andre C. Stiel wrote:
> Sorry, my mistake, I omitted the [p_ref], seemed starnge to me ... now
> it works to load into ccptraj. With ccptraj he does the tranlstion
> correctly with:
> rmsd reference .CA .CA out test.list out results
> What is "[p_ref]", could not find it in the manual ... stupid question I
> suppose.
>
> Thanks again Dan!
>
>
>
>
> 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 - 06:00:07 PDT
