ADL: Generate ligands pdbqt in batch mode [Raccoon]

Gianluca Interlandi gianluca at u.washington.edu
Mon Oct 5 22:14:25 PDT 2020


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




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