ADL: Attempting to create flexible portion of receptor for Autodock 4.2 and Autodock Vina

Tim M. timolivermaier at gmail.com
Thu Sep 10 21:13:34 PDT 2020


Hello Edmund,

I encountered the same error using current AutoDock Tools version with
Windows10. I reasoned that it might be an 32bit/64bit issue. It worked with
ubuntu for me. So if thats an option you can try using the Linux version.

Best Regards
Tim

Edmund Marinelli <edmundmarinelli at gmail.com> schrieb am Fr., 11. Sept.
2020, 05:00:

> I'm using Autodock Tools 1.57.  I prepared the receptor as appropriate and
> was able to write the PDBQT file using the File ....Save.....Write PDBQT.
> It seemed to work fine , giving the message that the Autodock atom types
> were added.  Then I wanted to create the flexible pdbqt file.  Note that
> you have to create the flexible pdbqt file before the rigid.  If you try to
> create the rigid pdbqt file first the program returns the message that the
> flexible pdbqt files must be prepared first.
>
> OK:  After writing the pbdqt for the receptor I did the following: Flexible
> residues -->  Input  --> Choose macromolecule.  I chose the macromolecule.
> Then in the dashboard I selected one residue as a test.  In the viewing
> pane the residue was highlighted.  With the residue highlighted I did the
> following:  Flexible Resides --> Choose torsions in currently selected
> residues.  The program immediately closed with no error message given.  I
> don't know if my procedure is   incorrect.  Has anyone else tried flexible
> docking using Autodock Tools version 1.57?
>
> Is there another way to do this ?  I would like to perform docking with
> flexible sidechains in the pocket residues of the receptor.  Has anyone
> been able to do this in Autodock 4.2 or in Autodock 4, or with Autodock
> Vina or with an earlier version of Autodock tools?
>
> Is there any worked example or tutorial out there?  Any help would be
> appreciated.
>
> If the syntax of a sample flexible.pdbqt file exists perhaps I would be
> able to use it to construct my own file , hence avoiding the problems of
> generating it from within Autodock tools ,  as there seems to be a
> problem.
>
> Ed
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