Hi Daniel,
My apologies that I wrote previous email while multitasking several
things. I have a system with protein ligand complex embedded in POPC
bilayer, ions and TIP3P. I monitored the changes in the volume of the
cavity occupied by the ligand from the trajectory and it seems the volume
is changing. It is expected in a membrane protein upon conformational
changes. I want to perform clustering so that I can visualise
representative members of the cluster and look at the change in the volume,
interactions of ligand with the protein in the pocket, etc.
Here is my cpptraj script
trajin xx.dcd 1 2500 2
strip :POP
strip :SOD
strip :CLA
autoimage
reference pro-ions-wat-lip.pdb //reference snapshot with everything
rms reference :1-441.CA,C,N,O // fit the protein
rms reference :LIG out lig_Rmsd.dat nofit //rmsd ligand but donot fit
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?
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)
>
> _______________________________________________
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> 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
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Received on Tue May 31 2016 - 18:30:02 PDT
