ADL: Generate ligands pdbqt in batch mode [Raccoon]

Gianluca Interlandi gianluca at u.washington.edu
Wed Oct 7 10:39:45 PDT 2020


Hi Francois,

Thanks for responding to my question. I figured out the best way to 
convert mol2 to pdbqt files from the command line by using (all in one 
line):

pythonsh <MGLTools installation 
path>/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py -l 
ligand_1.mol2 -v

`pythonsh` is also a program contained within MGLTools. I set it in my 
executable path.

I found that prepare_ligand4.py produces out of the box a pdbqt file that 
is actually more accurate than what you get when you use ADT without 
thinking much. When I first used ADT, I just loaded the ligand and saved 
it. In this way, ADT does not add Gasteiger charges (which by way the are 
not needed for AutoDock Vina), but also ADT does not automatically select 
the correct Root for the ligand. In ADT, you must go to Ligand -> Torsion 
Tree -> Detect Root. However, prepare_ligand4.py selects the correct Root 
by default and adds Gasteiger charges (again not needed for AutoDock 
Vina). prepare_ligand4.py also has several command line options to 
determine its behavior.

To answer your question about obabel. If you type `obabel -H pdbqt` it 
prints out options specific to the pdbqt format such as:

Write options, e.g. -xr, -xp, -xrp
   b  Enables automatic bonding before writing to pdbqt format
   r  Outputs rigid molecule (no branches)
   s  Outputs as a flexible residue
   p  Preserves the atom indexes from the input file
   (default is to renumber sequentially).

So "-xsp" would output a flexible residue and preserve the atom indexes. 
Again, I would not use obabel at this point, but prepare_ligand4.py. 
obabel also does not seem to have an option to add Gasteriger charges if 
you need them (you don't for AutoDock Vina).

As a side note: Raccoon also produces a pdbqt file that has the correct 
Root and Gasteiger charges by default, but if all you need is to convert a 
ligand file from the command line, then prepare_ligand4.py is what you 
need.

Thanks,

      Gianluca

On Wed, 7 Oct 2020, Francois Berenger wrote:

> On 07/10/2020 07:33, Gianluca Interlandi wrote:
>> I think I figured out how to make obabel write a pdbqt file that is
>> the same as what ADT would output, by using the flag: -xsp
>> 
>> obabel ligand_1.mol2 -O ligand_1.pdbqt -xsp
>
> What is the meaning of the -xsp option to obabel?
> I cannot find in the doc.
>
>> Then, I have to edit ligand_1.pdbqt to remove "BEGIN_RES" and
>> "END_RES" and add "TORSDOF". If anybody has any suggestions how to
>> make it more straightforward or any feedback whether any of this makes
>> sense, please let me know.
>
> If you provide and example input file and an example output file,
> I might send a shell script for that part.
>
> The fact that openbabel pdbqt output format is not compatible
> out of the box with autodock is quite annoying...
> I personally don't know of any tool (except autodock or vina) which requires 
> the pdbqt file format.
>
>> Gianluca
>> 
>> On Mon, 5 Oct 2020, Gianluca Interlandi wrote:
>> 
>>> OK, now I understand that there are different versions of Raccoon. I 
>>> downloaded the version from http://autodock.scripps.edu/resources/raccoon, 
>>> which is different than the version that came with MGLTools. This version 
>>> makes sense and I am generating pdbqt files.
>>> 
>>> However, I see that the pdbqt generated by Raccoon is different than the 
>>> one generated by ADT. This is the one from ADT:
>>> 
>>> REMARK  2 active torsions:
>>> REMARK  status: ('A' for Active; 'I' for Inactive)
>>> REMARK    1  A    between atoms: C5_4  and  P7_5
>>> REMARK    2  A    between atoms: P7_5  and  O10_8
>>> ROOT
>>> ATOM      1  C1  ZIN d   1      -0.019   1.526   0.010  0.00  0.00 0.090 C
>>> ATOM      2  C2  ZIN d   1       0.002  -0.004   0.002  0.00  0.00 0.130 A
>>> ATOM      3  O4  ZIN d   1      -0.748  -0.686   1.009  0.00  0.00 -0.330 
>>> OA
>>> ATOM      4  C5  ZIN d   1       0.672  -0.715   1.180  0.00  0.00 -0.500 
>>> A
>>> ENDROOT
>>> BRANCH   4   5
>>> ATOM      5  P7  ZIN d   1       1.390   0.318   2.500  0.00  0.00 2.270 P
>>> ATOM      6  O8  ZIN d   1       0.295   1.238   3.087  0.00  0.00 -1.080 
>>> OA
>>> ATOM      7  O9  ZIN d   1       2.529   1.182   1.915  0.00  0.00 -1.080 
>>> OA
>>> BRANCH   5   8
>>> ATOM      8  O10 ZIN d   1       1.976  -0.628   3.663  0.00  0.00 -0.900 
>>> OA
>>> ATOM      9  H14 ZIN d   1       2.374  -0.145   4.400  0.00  0.00 0.410 
>>> HD
>>> ENDBRANCH   5   8
>>> ENDBRANCH   4   5
>>> TORSDOF 2
>>> 
>>> This is the one from Raccoon:
>>> 
>>> REMARK  2 active torsions:
>>> REMARK  status: ('A' for Active; 'I' for Inactive)
>>> REMARK    1  A    between atoms: C5_4  and  P7_5
>>> REMARK    2  A    between atoms: P7_5  and  O10_8
>>> ROOT
>>> ATOM      1  P7  ZIN d   1       1.390   0.318   2.500  0.00  0.00 0.279 P
>>> ATOM      2  O8  ZIN d   1       0.295   1.238   3.087  0.00  0.00 -0.645 
>>> OA
>>> ATOM      3  O9  ZIN d   1       2.529   1.182   1.915  0.00  0.00 -0.645 
>>> OA
>>> ENDROOT
>>> BRANCH   1   4
>>> ATOM      4  C5  ZIN d   1       0.672  -0.715   1.180  0.00  0.00 0.270 A
>>> ATOM      5  C2  ZIN d   1       0.002  -0.004   0.002  0.00  0.00 0.160 A
>>> ATOM      6  C1  ZIN d   1      -0.019   1.526   0.010  0.00  0.00 0.043 C
>>> ATOM      7  O4  ZIN d   1      -0.748  -0.686   1.009  0.00  0.00 -0.362 
>>> OA
>>> ENDBRANCH   1   4
>>> BRANCH   1   8
>>> ATOM      8  O10 ZIN d   1       1.976  -0.628   3.663  0.00  0.00 -0.321 
>>> OA
>>> ATOM      9  H14 ZIN d   1       2.374  -0.145   4.400  0.00  0.00 0.221 
>>> HD
>>> ENDBRANCH   1   8
>>> TORSDOF 2
>>> 
>>> Thanks,
>>>
>>>     Gianluca
>>> 
>>> On Mon, 5 Oct 2020, Gianluca Interlandi wrote:
>>> 
>>>> Dear all,
>>>> 
>>>> I have learned to use AutoDock Vina to dock a ligand on a receptor. I 
>>>> used ADT to create a pdbqt file from the ligand mol2 file. I need to do 
>>>> the same for a few thousand ligands, which are individually stored as 
>>>> mol2 files. I started `raccoon` from the MGLTools package for Linux. I 
>>>> have the option to connect to a server, but the ligand files are on my 
>>>> workstation. The button for "Workstation" is grayed out and cannot click 
>>>> on it. How can I use raccoon to convert all mol2 files in a folder to 
>>>> pdbqt?
>>>> 
>>>> I also tried using openbabel, but the pdbqt file produced for a test file 
>>>> is different than the one produced by ADT. Is there a way to run ADT in 
>>>> batch mode?
>>>> 
>>>> Thanks,
>>>>
>>>>     Gianluca
>>>> 
>>>> -----------------------------------------------------
>>>> Gianluca Interlandi, PhD gianluca at u.washington.edu
>>>>                    +1 (206) 685 4435
>>>>                    http://gianluca.today/
>>>> 
>>>> Research Assistant Professor at the Department of Bioengineering
>>>> at the University of Washington, Seattle WA U.S.A.
>>>> -----------------------------------------------------
>>>> 
>>>> 
>>>> ________________________________________________
>>>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>>> 
>>>> 
>>> 
>>> -----------------------------------------------------
>>> Gianluca Interlandi, PhD gianluca at u.washington.edu
>>>                    +1 (206) 685 4435
>>>                    http://gianluca.today/
>>> 
>>> Research Assistant Professor at the Department of Bioengineering
>>> at the University of Washington, Seattle WA U.S.A.
>>> -----------------------------------------------------
>>> 
>>> 
>>> ________________________________________________
>>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>> 
>>> 
>> 
>> -----------------------------------------------------
>> Gianluca Interlandi, PhD gianluca at u.washington.edu
>>                     +1 (206) 685 4435
>>                     http://gianluca.today/
>> 
>> Research Assistant Professor at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------
>> 
>> 
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at u.washington.edu
                     +1 (206) 685 4435
                     http://gianluca.today/

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------




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