Dear Marc
Aha! I think I got it.
'closest' command modify coordinate frame *and topology* (not like
'strip') so write out the modified topology with 'parmwrite' and use the
modified topologies to load the produced trajectories right?
Thanks for the help!
Asai.
On 2015年01月31日 00:04, Marc van der Kamp wrote:
> You could keep a *specific number* of water molecules around each
> individual peptide in your "1 peptide" trajectories by using the "closest"
> command.
> --Marc
>
>
> On 30 January 2015 at 14:56, 浅井 賢 <suguruasai.gmail.com> wrote:
>
>> 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 - 07:30:04 PST
