ADL: "pdbcen" function

Antonio Cavazzuti acavazzuti at ipb.csic.es
Thu Mar 13 10:14:12 PDT 2008


Thank you very much Tee for the answer. 
The solution that you send me did not fix the problem. I ask to you a little
more patience..:)
I looked for pdbcen in my PC (find / -name pdbcen), but there is no file with
this name in the hard disk (just the link created with "ln -s
/usr/local/dist305/share/pdbcen pdbcen" in /usr/local/bin ) . 
Also I do not have /dist305 folder. Googleing "/dist305" I found only links to
Autodock3.* releases. Maybe the fact that I am using Autodock4 Autogrid4 and
ADT 1.5 (under Ubuntu 7.10) is part of the problem.. maybe an incomplete
installation..
Thank you one more time,
Antonio



> Message: 6
> Date: Wed, 12 Mar 2008 05:30:38 +0000 (GMT)
> From: Tee Pioj <tee_piorj at yahoo.com>
> Subject: Re: ADL: "pdbcen" function
> To: autodock at scripps.edu
> Message-ID: <447550.48503.qm at web59311.mail.re1.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
> 
> 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 ipb.csic.es>
> To: autodock at scripps.edu
> Sent: Tuesday, March 11, 2008 10:21:16 PM
> Subject: ADL: "pdbcen" function
> 
> Hi,
> 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,
> Antonio
> 
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