ADL: MGL Tools 1.5.7 and ADFR Suite 1.0 Issues and Development Paths

Edmund R Marinelli edmundmarinelli at gmail.com
Tue Oct 6 21:46:33 PDT 2020


MGL Tools 1.5.7: 

1.) When downloaded and installed (Windows version) the directory is labeled
MGL Tools 1.5.7.  However the splash screen and the desktop icon is titled
AutoDock Tools v 1.5.7.  A bit confusing because when the desktop AutoDock
Tools icon is clicked and the program opens one can see a tool bar for 
Ligand, Flexible Residues. Grid, Docking, Run and Analysis whose leftmost
portion lists that tool bar as ADT4.2.  Presumably ADT4.2 means AutoDock
Tools 4.2.  So the versioning and program nomenclature seems inconsistent.  

2.) Using ADT 1.5.7 the Sequence viewer area is empty after importing or
reading a PDB file from RCSB into ADT 1.5.7.  I've tried a number of PDB
files from RCSB and in all cases the sequence viewer is not populated with
the sequence.  

3.) Activating the AutoDockFR tool bar by clicking the FR button in the
uppermost toolbar gives the AutoDockFR toolbar beneath the ADT4.2 menu bar. 
Clicking 'Receptor' menu item reveals that the desired receptor can only be
accessed as an XML file, whereas 'Ligand' can be accessed as an XML file or
as a PDBQ file.  *Question:* Is the plan to move eventually to XML for both
receptor and ligand? *Question:* With respect to 'Ligand' menu item: Why is
PDBQ used as opposed to PDBQT as the alternate file format to XML?  *Also:*
If, eventually, XML is to be used exclusively for receptor and ligand files
will there be a need to tools to convert PDB files to XML format? 

4.) Clicking on the 'Docking' menu item of the AutoDockFR menu reveals
provides 'Run' in the dropdown, which when clicked gives and 'Under
Construction' message - I realize that ADT v 1.5.7 is a work in progress. 

*In re ADFR Suite 1.0:*

5.) The AGFR 1.0 (Built Oct 28 _19) from the ADFR Suite 1.0 is a very
interesting, compact and powerful graphical interface for generating the
grid maps for ADFR: *Question:* Is the combination of AGFR 1.0 (Built Oct 28
_19) graphical interface and command line execution of ADFR to be 
superseded by the molecular docking tools of ADT 1.5.7?  It appeared to me
that AGFR 1.2, which includes Autosite 1.0 could be expanded to include a
graphical interface to AutoDock FR and perhaps to AutoDock Vina that could
obviate the need for execution of the docking from a command line.  I am
trying to understand whether the docking facilities in MGL Tools 1.5.7 (aka
ADT 1.5.7) and ADFR Suite 1.0 are parallel development paths or is one going
to be superseded by the other?



  



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