Hi,
On Tue, May 31, 2016 at 7:28 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> cluster C0 out cnumvtime.dat summary summary.dat info info.dat rms mass
> nofit :LIG clusters 10 clusterout cluster clusterfmt pdb repout
> representative repfmt pdb
>
> Is this the right way of clustering based on the ligand pocket?
This will cluster based on the movement of the ligand with respect to
your last RMS-fit (in this case the backbone atoms of residues 1-441),
which may indeed be what you want. If you want to cluster based on
pocket volume you would need to load that data in and cluster on that
as I previously described. Hope this helps,
-Dan
>
> I hope I am able to explain the scenario.
>
> Many thanks,
> Neha
>
>
>
> On 1 June 2016 at 01:00, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> I'm not sure I completely understand what you want to do, but if you
>> have an existing data set you would like to use for clustering you can
>> read it in with the 'readdata' command and cluster using that data via
>> the 'cluster' command and the 'data' keyword. See the manual for more
>> details.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Sun, May 29, 2016 at 7:12 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>> > Dear List,
>> >
>> > I want have trajectory with ligand complexed to the protein. I have
>> > measured the volume of the cavity within 10A from the ligand. I want now
>> > perform clustering based on the distance 10A from the ligand present in
>> the
>> > trajectory.
>> >
>> > How can I achieve this?
>> >
>> > I have so far loaded the trajectory, removed ions, water etc. Done
>> > autoimage.
>> >
>> > Awaiting your feedback.
>> >
>> > --
>> > Regards,
>> > Dr. Neha S. Gandhi,
>> > Vice Chancellor's Research Fellow,
>> > Queensland University of Technology,
>> > 2 George Street, Brisbane, QLD 4000
>> > Australia
>> > LinkedIn
>> > Research Gate
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 01 2016 - 08:00:04 PDT
