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
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Mon Aug 02 2010 - 09:00:09 PDT
