AMBER Archive (2008)

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

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Tue May 27 2008 - 11:03:54 CDT

On 5/27/08, Jianyin Shao <jyshao2004_at_gmail.com> wrote:
>
>
>
> On 5/25/08, Dong Xu <d1xu_at_ucsd.edu> wrote:
>>
>> Hi Jianyin Shao,
>>
>> The silhouette.pl 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.

Jianyin

> go
>

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