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
>>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 02 2010 - 11:00:05 PDT
