ADL: why cluster rmsd =0 ?

Bjoern Olausson olausson at
Fri Mar 28 03:27:21 PDT 2008

On 3/28/08, qiaoyan <qiaoyan at> wrote:
>  Another question:
>  How to save the docked conformation as pdb ?
>  Please help me.thank you !

Thats a really good question.

You could try the following... but didn't work for me:
- Open "clustering --> show"
- Choose a cluster
--> conformation player will open
- Hit the "&"
- select "write complex"
- close your analyze
- read the newly written complexed pdbqt
- select "File --> Save --> Write PDB"
(Not shure which options to choose... but no combination resulted in a
working PDB file for sybyl pymol, thought works fine on these pdb

converting this PDB to MOL2 with openbabel makes babel fail with
"Speicherzugriffsfehler" (Memory access failure)

Please let me know if you found a way to get a working pdb file.

kind regards

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