Hello,
You'd still use the same syntax that Dan described to you, you just have to
specify the mask to include only the atoms you want. The only way to get
concatenated coordinates is to use a trajectory file type for the trajout
file. Alternatively you can catenate each PDB to the end of the one that
came before to get a single file.
The strip command would look something like this:
strip !(:1.CA)
if, for instance, you only wanted to track the carbon alpha of the first
residue of the system. Then use an mdcrd file as the trajout type:
trajout file.mdcrd
Since all that's left is the CA of the residue you want, you will see only
the XYZ of the CA on each line. Whatever route you choose to take, it
sounds like you'll have to script some of the analysis yourself afterwards.
Good luck!
Jason
On Mon, Aug 2, 2010 at 1:38 PM, Ibrahim Moustafa <I.moustafa.psu.edu> wrote:
> Hi Daniel,
>
> Many thanks for the reply. Actually, this did not do what I want. It
> created output frames with all CA atoms in each frame. I wanted to create
> files for each CA atom with concatenated coordinates corresponding to the
> time evolution of the different frames.
>
> Thanks,
> Ibrahim
>
>
> On 8/2/10 11:43 AM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > You can accomplish this in ptraj by using the "strip" command to strip
> > all atoms except the CA atoms, e.g.
> >
> > strip !(.CA)
> >
> > Then write out pdb files with "trajout",
> >
> > trajout file.pdb pdb
> >
> > See the manual for more detailed descriptions of these commands.
> >
> > -Dan
> >
> > On Monday, August 2, 2010, Ibrahim Moustafa <I.moustafa.psu.edu> wrote:
> >> Dear Users,
> >>
> >> I have an Amber trajectory (10 ns) of an entire protein structure of
> 400
> >> atoms. What Iım looking for is a way to write out the coordinates for
> each
> >> C-alpha along the trajectory in a single file with the same order; i.e.,
> >> coordinates of frame1 precedes that of frame2..etc. The format of the
> output
> >> file does not really matter whether it is pdb or just separate fields
> for X,
> >> Y and Z. In other words, I want to have 400 files, each file has the
> lines
> >> corresponding to the C-alpha coordinates through the trajectory
> timeline.
> >>
> >> I wonder if there is a way to do such analysis in Ptraj? Or any
> >> suggestions.
> >>
> >> Thanks in advance for help,
> >>
> >> Ibrahim
> >>
> >> --
> >>
> >> Ibrahim M. Moustafa, Ph.D.
> >> Biochemistry and Molecular Biology Dept.
> >> 201 Althouse Lab., University Park,
> >> Pennsylvania State University
> >> PA 16802
> >>
> >> Tel. (814) 863-8703
> >> Fax (814) 865-7927
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Aug 02 2010 - 12:00:03 PDT
