Subject: Re: CCL:Query regarding AutoDock software.

From: "Flight, Robert Maxwell" <l72k6[at]unb.ca>
Date: Wed, 28 Apr 2004 13:52:12 -0300

Hi Raju,

The PDB file from the docking log (get-dockings) command will have the ligands in the
same orientation with respect to the macromolecule.  You must load the original file
(PDB, MOL2, etc) of the macromolecule that you used to create the PDBQS in order to
view the interactions of the ligands with the receptor.  

-Robert

***************************
Robert Flight
Master Candidate
Computational Chemistry
Department of Chemistry
University of New Brunswick
Fredericton  NB, Canada  E3B 6E2
e-mail: robert.flight[at]unb.ca
***************************
"A computer terminal is not some clunky old television with a typewriter in front of
it.
 It is an interface where the mind and body can connect with the universe and move bits
of it about." -- Hitch Hikers Guide to the Galaxy

Quoting Raju Vishwanathan <raju.v[at]sysarris.soft.net>:

> Problem with AutoDock 3.0.5. Installed AutoDock in Red Hat Linux 8.0.
> 
> AutoDock FAQ point no 3 says "I used "get-dockings" to extract the docked
> conformations. Where is the macromolecule?"
> http://www.scripps.edu/pub/olson-web/doc/autodock/faq.html#WHERE_MACRO
> 
> 
> 	$ get-dockings xk2A.1hvr.dlg    { Its working, generates output file
> xk2A.1hvr.dlg.pdb }
> 	$ pdbqtopdb 1hvr.pdbqs >> xk2A.1hvr.dlg.pdb      { Not working, shows the
> following error}
> 
> 	awk: /home/raju/src/autodock/dist305/share/pdbtopdb2.awk:49: fatal: Invalid
> range end: /[0-9][+- ]/
> /home/raju/src/autodock/dist305/share/fixatomnames: line 8:  1839 Broken
> pipe
>           sed -f $AUTODOCK_UTI/fixatomnames.sed $*
> /home/raju/src/autodock/dist305/share/getpdbrecords: line 2:  1840 Broken
> pipe
>            egrep "^ATOM|^HETATM|^REMARK|^USER|^END |^TER|^MODEL |^ENDMDL" $*
> 
> I donot know how to solve this problem. Please let me know how to overcome
> this problem.
> 
> Thanking you,
> Raju Vishwanathan
> Sr. Consultant - Life Science Division
> SysArris Software, Bangalore, India
> 
> 
> 
> 
> 
> 
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