AMBER Archive (2008)

Subject: Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9

From: Jianyin Shao (
Date: Tue May 27 2008 - 10:37:57 CDT

On 5/25/08, Dong Xu <> wrote:
> Hi Jianyin Shao,
> The script works great!
> A question about decoy:
> First I run averagelinkage to determine the cluster count and to
> obtain the cluster representatives. Then I use the cluster count and
> the cluster representatives from averagelinkage as the seed structures
> for decoy. You mention that decoy_structure file should be a
> trajectory file. Does it have to be in amber mdcrd format? What's the
> best way to convert multiple pdb file to an amber (or maybe other)
> trajectory file that is accepted by decoy?

 You can use another ptraj script:
trajin pdb1.pdb
trajin pdb2.pdb
trajin pdb3.pdb
trajout decoy.ptraj pdb

> On Fri, May 23, 2008 at 8:08 PM, Dong Xu <> wrote:
> > 2nd question. If I want to generate clustering statistics plots like
> > DBI vs. cluster count, pSF vs. cluster count, similar to Figure 8 and
> > Figure 10 in your paper, do I have to run clustering 10 times with
> > different cluster count 1 thru 10? If so, does this apply to all
> > algorithms such as average linkage, means etc.?
> >

Yes. I will do the clustering 10 times. I am thinking a way to consolidate
the runs.

> On Fri, May 23, 2008 at 7:07 PM, Dong Xu <> wrote:
> >> Hi Jianyin,
> >>
> >> A quick question for you. I have to rms fit my MD trajectory in ptraj
> >> to a reference structure before clustering, correct? If so, can I do
> >> both rms fit and clustering in the same ptraj run or separate runs?
> >>
You can do the rms fitting and clustering in the same ptraj script.



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