ADL: Generate ligands pdbqt in batch mode [Raccoon]

Gianluca Interlandi gianluca at u.washington.edu
Tue Oct 6 15:33:59 PDT 2020


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

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.

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.
-----------------------------------------------------




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