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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