ADL: "pdbcen" function

Tee Pioj tee_piorj at
Tue Mar 11 22:30:38 PDT 2008

Hello, Antonio Cavazzuti 
Again you  should solve this problem with these command:

$cd /usr/local/bin

and then 

$ln -s /usr/local/dist305/share/pdbcen pdbcen

This commamd is a link command (ln). This put link of pdbcen command into bin directory. Try typing pdbcen again. It gonna work.

Best luck,
Tee Piroj

----- Original Message ----
From: Antonio Cavazzuti <acavazzuti at>
To: autodock at
Sent: Tuesday, March 11, 2008 10:21:16 PM
Subject: ADL: "pdbcen" function

I am using Autodock4 Autogrid4 and ADT 1.5 under Ubuntu. I had problems with
grid setting up. Tee Piroj (thanks you!!) previously suggested me to use
"pdbcen" command to obtain center of binding site and put them in grid
dialogue box. 
Finally I had to manually calculate center of binding site because "pdbcen"
doesn't work.. I open a terminal windows, I change directory where my pdb file
is and I enter

pdbcen myfile.pdb

...but the answer is "command not found"

How can I solve this? 
Thanks in advance,

Instituto de Parasitologia y Biomedicina "Lopez-Neyra"
Avda. Conocimiento S/N
Parque Tecnologico Ciencias de la Salud
18100 Armilla - GRANADA
Tlf: 958181621
Fax: 958181632

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