ADL: Generate ligands pdbqt in batch mode [Raccoon]

Francois Berenger mlists at ligand.eu
Tue Oct 6 23:46:00 PDT 2020


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 
> ---




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