On 5/27/08, Jianyin Shao <jyshao2004.gmail.com> wrote:
>
>
>
> On 5/25/08, Dong Xu <d1xu.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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Received on Wed May 28 2008 - 06:07:53 PDT
