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

Michel Sanner sanner at scripps.edu
Fri Sep 11 08:30:57 PDT 2020


Hi Ed

You can you AutoGridFR (AGFR) to prepare your receptor (with flexible side chains) and generate the AutoDock affinity maps. AGFR will generate a .trg file which you can use directly for docking with AutoDockFR (ADFR) or you can unzip to extract the actual affinity maps that you can use with AutoDock4.

You can download the ADFRsuite at https://ccsb.scripps.edu/adfr/downloads/ (contains both AGFR and ADFR among other tools)

There is a tutorial for preparing maps for a receptor with flexible side chains at https://ccsb.scripps.edu/adfr/documentation/

I hope this helps

-Michel

From: <autodock-bounces at scripps.edu> on behalf of Edmund Marinelli <edmundmarinelli at gmail.com>
Reply-To: "autodock at scripps.edu" <autodock at scripps.edu>
Date: Thursday, September 10, 2020 at 7:59 PM
To: "autodock at scripps.edu" <autodock at scripps.edu>
Subject: ADL: Attempting to create flexible portion of receptor for Autodock 4.2 and Autodock Vina

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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