ADL: pdbqt to pdb

Collignon, Barbara C. collignonbc at
Sun Apr 5 11:59:12 PDT 2009

I already use pymol :). 

What I need, it is just to do:
foreach file(ls *pdbqt)
./script_pdbqt_to_pdb -v $file

babel -ipdb *pdb -osdf allfiles.sdf
I did it, but I am unable to read the sdf with pymol.

So I tried to figure out why. I believed that could be
an error when generating the pdb from the pdbqt. That
why I was asking for other scripts.

Or could it be a missing plug-in in the free version of pymol ?


-----Original Message-----
From: autodock-bounces at on behalf of Franck Vendeix
Sent: Sat 4/4/2009 9:55 AM
To: autodock at
Subject: Re: ADL: pdbqt to pdb

I suggest the use of the free version of Pymol (

> Date: Fri, 3 Apr 2009 18:06:14 -0400
> From: collignonbc at
> To: autodock at
> Subject: ADL: pdbqt to pdb
> Do someone know, how to convert a pdbqt file into a pdb file
> without using or cut -c-66 $f.pdbqt > $f.pdb ?
> Is a script available somewhere ?
> Barbara C. Collignon, Ph.D
> Center For Molecular Biophysics
> Post-doctoral Research Fellow
> UT-Oak Ridge National Laboratory
> Building 6011, Mail Stop 6309
> Oak Ridge, TN  37831-6309
> ________________________________________________
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