ADL: get-dockings in AD4

Josmar R. da Rocha bije_br at yahoo.com.br
Wed Jan 23 08:19:59 PST 2008


Dear Antje,

Humm!! I hadn't noticed it. In fact, my ligands does not have clorides. Anyway, you can modify the 3th line to:
grep '^DOCKED' my_docking.dlg | cut -c9-| sed -e 's/\sL/CL/g'> my_docking.pdbqt

However, take care with bromides too. Maybe is necessary to add an additional "sed" in the 3th line.

 I hope it helps!

 Josmar Rocha
 Universidade de Sao Paulo - USP
 Instituto de Quimica de Sao Carlos
>NEQUIMED
 Sao Carlos - SP


Message: 6
Date: Tue, 22 Jan 2008 11:42:50 +0100
From: Antje Wolf 
Subject: Re: ADL: get-dockings in AD4
To: autodock at scripps.edu
Message-ID: <4795C8AA.3060906 at scai.fraunhofer.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Dear Josmar,

nice script. Thanks. This is exactly what I was looking for.

But it is not preserving the atom types correctly. If you have e.g. a 
chlorine atom, then the /C/ of /Cl/ is cut and only the /l/ is preserved 
(because of a column shift). This is the same mistake /get-dockings/ is 
doing. Did you notice that?

Antje


       
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