ADL: Question about Autodock4Zn

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ADL: Question about Autodock4Zn

Ren Xiaodong


Hi,


I am a novice of the Autodock4Zn, Can I ask a question about it?


When I followed the tutorial to execute the following commands using the protein.pdb included in the tutorial:


$MGLROOT/bin/pythonsh prepare_receptor4.py -r protein.pdb -o protein.pdbqt

$MGLROOT/bin/pythonsh zinc_pseudo.py -r protein.pdbqt -o protein_tz.pdbqt

I can get the feedback of "Wrote 1 TZ atoms on protein_tz.pdbqt".


But when I used another protein downloaded from PDB bank (PDB ID:4gwm), there seems some problem with the zinc_pseudo.py.

I firstly processed the 4gwm.pdb, keeping only the protein chain A and Zn to give 4gwm_clean.pdb. then I run the following two commands;


$MGLROOT/bin/pythonsh prepare_receptor4.py -r 4gwm_clean.pdb -o 4gwm_clean.pdbqt

$MGLROOT/bin/pythonsh zinc_pseudo.py -r 4gwm_clean.pdbqt -o 4gwm_clean_tz.pdbqt


After that, I got the feedback of  "Wrote 0 TZ atoms on 4gwm_clean_tz.pdbqt.", which means this step failed.

I also tried other zinc-contating proteins, but all failed with "Wrote 0 TZ atoms..." .  attached is the three files of 4gwm.

Can any experienced users help me to fix the problem?

Best wishes
Xiaodong Ren


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4gwm_clean 1.pdbqt (482K) Download Attachment
4gwm_clean 1.pdb (488K) Download Attachment
4gwm_clean_tz 1.pdbqt (482K) Download Attachment
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Re: ADL: Question about Autodock4Zn

Diogo Martins
Hi Xiaodong Ren,

The TZ pseudo-atom is added to zinc atoms that are coordinated by exactly
three protein residues. It defines the position where a ligand atom may
coordinate the zinc atom in a tetrahedral geometry.

In structure 4gwm, zinc is already coordinated by four protein residues. If
a ligand were to coordinate to zinc, it would become penta-coordinated.
Therefore, the TZ pseudo-atom is not added.

Let me know if you have further questions.

Good luck!

On 11 June 2017 at 09:12, Ren Xiaodong <[hidden email]> wrote:

>
>
> Hi,
>
>
> I am a novice of the Autodock4Zn, Can I ask a question about it?
>
>
> When I followed the tutorial to execute the following commands using the
> protein.pdb included in the tutorial:
>
>
> $MGLROOT/bin/pythonsh prepare_receptor4.py -r protein.pdb -o protein.pdbqt
>
> $MGLROOT/bin/pythonsh zinc_pseudo.py -r protein.pdbqt -o protein_tz.pdbqt
>
> I can get the feedback of "Wrote 1 TZ atoms on protein_tz.pdbqt".
>
>
> But when I used another protein downloaded from PDB bank (PDB ID:4gwm),
> there seems some problem with the zinc_pseudo.py.
>
> I firstly processed the 4gwm.pdb, keeping only the protein chain A and Zn
> to give 4gwm_clean.pdb. then I run the following two commands;
>
>
> $MGLROOT/bin/pythonsh prepare_receptor4.py -r 4gwm_clean.pdb -o
> 4gwm_clean.pdbqt
>
> $MGLROOT/bin/pythonsh zinc_pseudo.py -r 4gwm_clean.pdbqt -o
> 4gwm_clean_tz.pdbqt
>
>
> After that, I got the feedback of  "Wrote 0 TZ atoms on
> 4gwm_clean_tz.pdbqt.", which means this step failed.
>
> I also tried other zinc-contating proteins, but all failed with "Wrote 0
> TZ atoms..." .  attached is the three files of 4gwm.
>
> Can any experienced users help me to fix the problem?
>
> Best wishes
> Xiaodong Ren
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---