Hi Jianyin,
Thanks for the detailed and prompt reply.
In my analysis, I found that there are 5 clusters and the last one has more
number of points.
I took the representative pdb from that cluster and used as a reference and
calculated RMSD for
all the other points in the cluster. I was expecting very low RMSD, but almost
all points
have RMSD > 1 to this representative structure.
Can you guide me how to interpret this result?.. It would be great if you can
suggest me
better methods,(if any) to efficiently use this program.
I would be very thankful if anyone can point me best available methods to
analyze trajectories.
My ultimate goal is to get a representative structure that is very close to
time-average structure ( I am aware
that time-average structure is kind of meaningless in terms of coordinates)
thanks,
Senthil
Hi Senthil,
Unfortunately, you cannot visualize the ClusterMerging.txt by xmgrace. Each
line of this file records one step of merging. The first number should be a
negative number, which represents the newly formed node. The next two
numbers are the nodes to be merged, if a number is positive, that is the
frame number in the trajectory. The fourth number is distance between the
two nodes. The next two numbers are the DBI and pSF values for current
clustering. The DBI value will not be calculated if cluster number is larger
than 50. If you want to plot the cluster # vs. DBI or pSF, you can get the
values from the ClusterMerging.txt file without run multiple clustering
processes.
If you use sieve, the cluster merging is executed only in the first scan,
i.e. 1 frame out of every 10 frames in your case. The rest of frames will be
assigned to the closest cluster out of the 5 clusters formed in the first
scan. Thus, information in the ClusterMerging.txt would be irrelevant to the
entire trajectory.
Hope this helps,
Jianyin Shao
On Wed, Sep 1, 2010 at 3:14 PM, Senthil Natesan <sen.natesan.yahoo.com>wrote:
>
> Hi Amber Users,
> Greetings.
> Can someone please let me know how to visualize and infer the output file
> (ClusterMerging.txt)
> from ptraj-cluster program ?
>
> I just fired up the file with xmgrace and I don't get much.
>
> FYI:
> I have run a MD simulation of protein-ligand complex and used cluster
> program from ptraj for getting representative and average structure of the
> MD
> run.
> I used averagelinkage method for clustering. Clustering process went well.
> I
> used the
> following command in ptraj
>
> cluster out mk2mdrun all amber representative pdb average pdb
> averagelinkage
> sieve 10 clusters 5 rms mass :1-300
>
> Thanks in advance.
>
> Senthil Natesan
>
>
>
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Received on Wed Sep 01 2010 - 16:30:04 PDT
