ADL: pdbqt to pdb

bagdevi.mishra at gmail.com bagdevi.mishra at gmail.com
Sun Apr 5 23:35:53 PDT 2009


Barbara,

here is a perl code

---------------------
foreach $file(`ls *pdbqt`)
{
system ("pdbqt_to_pdb.py -f $file");
}
system ("babel -ipdb *.pdb -osdf allsdf.sdf --join");
---------------------

this works fine for the purpose as you have asked.

Did you use the pdbqt_to_pdb.py code for converting the pdbqt files to pdb ?
And if it worked fine, use --join option in babel to join multiple input
files into one output.

Regards,
Bagdevi Mishra.



On Mon, Apr 6, 2009 at 12:29 AM, Collignon, Barbara C. <collignonbc at ornl.gov
> wrote:

> I already use pymol :).
>
> What I need, it is just to do:
> ====================================
> foreach file(ls *pdbqt)
> ./script_pdbqt_to_pdb -v $file
> end
>
> 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 ?
>
>
> Barbara
>
>
> -----Original Message-----
> From: autodock-bounces at scripps.edu on behalf of Franck Vendeix
> Sent: Sat 4/4/2009 9:55 AM
> To: autodock at scripps.edu
> Subject: Re: ADL: pdbqt to pdb
>
>
> I suggest the use of the free version of Pymol (
> http://pymol.sourceforge.net/)
>
> > Date: Fri, 3 Apr 2009 18:06:14 -0400
> > From: collignonbc at ornl.gov
> > To: autodock at scripps.edu
> > Subject: ADL: pdbqt to pdb
> >
> >
> > Do someone know, how to convert a pdbqt file into a pdb file
> > without using pdbqt_to_pdb.py 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
> >
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
> _________________________________________________________________
> View your Twitter and Flickr updates from one place - Learn more!
> http://clk.atdmt.com/UKM/go/137984870/direct/01/
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


More information about the autodock mailing list