ADL: Preparing PDBQT files

annalisa bordogna annalisa.bordogna at
Tue Sep 28 01:15:49 PDT 2010


I answer with the whole autodock list in cc, since this information can be
valuable also for other people.

First: any pdb file is a text file. So, if you want to modify it, you can
easily open it in a text editor and change it (for example, if you want to
take onlly the protein, you can delete the lines of the ligand).

For your ligand: I don't use ChemDraw, so I really cannot give you any
information about how to convert the format. But I'm sure that in the net
you can find a server that makes this kind of stuff.


2010/9/28 Sanjiv Yadav <sanyad74 at>

> Hi Annalisa!
> Thanks for sharing your knowledge.
> I am just wondering if you can help me as I am quite new for Autodock
> software.
>  I want to  see the interaction of my small molecule (ligand) with
> PPARgamma protein (receptor). To do that I need to convert receptor  well as
> ligand PDB files into pdqt files first.
> My question(s):
> 1) How to get the only PPARgamma protein structure to refine and convert it
> into PDBQT from Protein data bank?
> Here what I tried: I pull out the Jmol pic of PPARg protein (from here *
> DOI:*10.2210/pdb3lmp/pdb <>) and save
> it in PDB file. Now I open the  AutoDoc 1.5.4 software and convert  this
> file into PDBQT and save it. This is my receptor PDBQT file.
> Confusion:  Although I save it as PDBQT file but I guess ligand is already
> with this PDBQT file? How to remove the ligand from this PDB/PDBQT file? So
> that I would be able to dock my ligand onto this PDBQT PPARg protein.
> 2)   For my Ligand: I have ligand which I draw in chemDraw software (
> .cdx). This ligand should first convert into PDB and then i should be able
> to make its PDBQT file. Now How to do this?
> 3) In next conversation after 2 points solved.
> Hope you would not mind to share with me. Thanks.
> With regards
> Sanjiv
> Hello,
> why don't you try some protein-protein docking servers, instead?
> For example:
> This is a protein-protein docking methods that requires some experimental
> data (e.g. NOE, RDC, mutations or even interface prediction) in input. It
> has several energy minimization cycles, thus treats the proteins as
> flexible:
> - ZDOCK (
> This is a FFT protein-protein docking method. It is very fast and complete
> and it does not need any additional input data. To be like this, it treats
> the proteins as rigid.
> Hope it helps!
> Cheers,
> Annalisa

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