ADL: get-dockings in AD4

Josmar R. da Rocha bije_br at yahoo.com.br
Sat Jan 19 12:08:09 PST 2008


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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