ADL: get-dockings in AD4

Antje Wolf antje.wolf at scai.fraunhofer.de
Tue Jan 22 02:42:50 PST 2008


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

Josmar R. da Rocha schrieb:
> Dear Antje Wolf
>
> I use this:
>
> #!/bin/csh
> #Extracting Docked from DLG Files
> grep '^DOCKED' my_docking.dlg | cut -c9- > my_docking.pdbqt
> #Converting from PDBQT to PDB
> cut -c-66 my_docking.pdbqt > my_docking.pdb
> #Splitting a Multi-Model PDB File into Separate PDB Files
> set a=`grep ENDMDL my_docking.pdb | wc -l`
>     set b=`expr $a - 2`
>     /usr/bin/csplit -k -s -n 3 -f my_docking. my_docking.pdb '/^ENDMDL/+1' '{'$b'}'
>     foreach f ( my_docking.[0-9][0-9][0-9] )
>       mv $f $f.pdb
>     end
>
> I hope it helps!
>
> Josmar Rocha
> Universidade de Sao Paulo - USP
> Instituto de Quimica de Sao Carlos
> NEQUIMED
> Sao Carlos - SP
>
>
>  Message: 5
> Date: Fri, 18 Jan 2008 17:43:30 +0100
> From: Antje Wolf 
> Subject: ADL: get-dockings in AD4
> To: autodock at scripps.edu
> Message-ID: <4790D732.7030900 at scai.fraunhofer.de>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
> Can I use get-dockings (from AutoDock3) on the dlg files of AutoDock4? I 
> am uncertain because of the atom types.
>
> Or is there another way of extracting the conformations? These scripts 
> like write_lowest_energy_ligand.py are saving the coordinates only in 
> pdbqt format. I need them in pdb or mol2.
>
> Any idea or experience?
>
> Thanks,
> Antje
>
>
>        
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