AMBER Archive (2008)

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

From: Jianyin Shao (
Date: Tue May 27 2008 - 11:03:54 CDT

On 5/27/08, Jianyin Shao <> wrote:
> 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

Oops. Should not specify pdb when outputting trajectory file.
Use "trajout decoy.ptraj" instead.

Sorry for the mistake.


> go

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