Hi Jason,
Many thanks for your input. This has worked, I just need to script it to go
over each C-alpha.
Many thanks,
Ibrahim
On 8/2/10 2:35 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
> 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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>>
>
>
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Received on Mon Aug 02 2010 - 12:00:08 PDT
