Dear Marc,
I see. Hum then what happen If I want to keep a peptide and water
molecules (which start from residue id 501 or so on)?
I'd like to analyze the water dynamics around each clusters as well.
Only the way I know is to use trajectory files which produced via
'clusterout' option of 'cluster' command.
Thanks a lot
Regards
Asai
On 2015年01月30日 23:50, Marc van der Kamp wrote:
> Dear Asai,
>
> If you strip out only one peptide (be it :1-10, :11-20, :21-30 etc.), all
> the trajectories (just xyz coordinates) can be read in by first reading in
> a prmtop file with only one peptide in it.
> So after reading in the different trajectories in cpptraj (on top of the
> prmtop file), you would only have residues :1-10.
>
> Hope that helps,
> Marc
>
> On 30 January 2015 at 14:45, 浅井 賢 <suguruasai.gmail.com> wrote:
>
>> Dear Marc
>>
>> Thanks for your suggestion. If I understood correctly, I think I need to
>> re-organize residue ID of each copies in each produced trajectories to
>> specify all copies in 'cluster' command with a single amber mask (e.g
>> ':1-10') right? Then how can I do it? Or is it ok to specify the
>> molecules as ':1-10,11-20,21-30,...' (or ':1-500') while each frames
>> only have a single copy?
>>
>> Thanks again for your reply.
>>
>> Best regards
>>
>> Asai
>>
>> On 2015年01月30日 21:41, Marc van der Kamp wrote:
>>> I would simply write out trajectories with just one copy (using the
>>> appropriate "strip" command in cpptraj), do this for all 50 copies, and
>>> then read in the trajectories (with ONLY your peptide, no water etc.)
>> back
>>> into cpptraj for clustering.
>>> Hope this helps,
>>> Marc
>>>
>>> On 30 January 2015 at 12:06, 浅井 賢 <suguruasai.gmail.com> wrote:
>>>
>>>> Dear AMBER users
>>>>
>>>> I'm using Amber 14 and I'm trying to cluster 50 copies of a single
>>>> molecule (very short peptide).
>>>> I know that I can cluster a single molecule in the trajectory via
>>>> 'cpptraj' as:
>>>>
>>>> cluster clusters 10 rms :1-10 out cluster.log ...
>>>>
>>>> But my system has 50 copies of the molecule (:1-10, :11-20, :21-30, ...)
>>>> and I'd like to find the difference not only between frames but also
>>>> between these copies of each frames.
>>>> Is there any way to do it? Any recommendations will be appreciated.
>>>>
>>>>
>>>> Thanks.
>>>>
>>>>
>>>> ---
>>>> Laboratory of Plasmamembrane and Nuclear Signaling, Graduate school of
>>>> Biostudies, Kyoto University.
>>>>
>>>> Suguru ASAI
>>>>
>>>> Tel: +81-75-753-7906
>>>> Fax: +81-75-753-7906
>>>> E-mail: asai.suguru.86x.st.kyoto-u.ac.jp
>>>> URL: http://www.lif.kyoto-u.ac.jp/labs/chrom/
>>>> Address: Room 419, Faculty of Medicine Bilding G (South Campus Research
>>>> Bilding), Yoshida Konoemachi, Sakyo-ku, Kyoto, Japan
>>>>
>>>>
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Received on Fri Jan 30 2015 - 07:00:05 PST
