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 - 07:00:04 PST
