Re: CCL:autodock3 dies upon launch with multiple errors

 Dear Robyn:
 In a command window in IRIX,
 try,
 # mkdpf3 <ligand_name>.pdbq  <enzyme_name>.pdbqs
 this will produce a <ligand>.<enzyme>.dpf file, then
 try
 # autodock3 -p <ligand>.<enzyme>.dpf -l
 <ligand>.<enzyme>.dlg&
 This might work if ADT could not launch the job.
 Cheers
 Yong
 On Fri, 17 Jun 2005, Robyn Ayscue wrote:
 
 All,
 Sorry for the cross-post.
 I'm running AutoDockTools using autodock/autogrid
 version 3.05 on an SGI machine with IRIX 6.5.24. I'm
 trying to dock an effector molecule in the active site
 of an enzyme (p450 2c9) with a substrate molecule also
 present. Autogrid finishes out with no problems, but
 autogrid dies immediately upon launch with the
 following errors:
 Can't find ".dpf" in the dock-parameter filename.
 AutoDock needs the extension of the grid parameter
 file to be ".gpf"
 and that of the docking parameter file to be ".dpf".
 /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3:
 Wrong number of x grid-points in grid-map file
 "2c9q_HEMq_FLPq.A.map".
 /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3:
 Use either 32 or 1129013060 throughout!
 /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3:
 ERROR: Using wrong grid-map file.
 /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3:
 Aborting...
 /disk02/usr/local/autodock/dist305/bin/sgi4D.IRIX64_6.5_R10000/autodock3:
 Unsuccessful Completion.
 First it complains about not being able to find a
 docking parameter file with .dpf as the suffix, but
 the file DOES have a .dpf suffix and it is listed as
 having one in the command that is typed in the command
 line used to launch autodock. The .dpf file looks fine
 as far as I can tell, compared to other .dpf files
 I've used for other docking runs that have completed
 successfully.
 The next thing it complains about is the differing
 number of grid points. It keeps referring to the
 number "1129013060" but I can't find that number in
 any of the grid-map files. The number of x- grid
 points in all grid-map files is the same.
 Autodock comes to the conclusion that I'm using the
 wrong grid-map files, but the files I'm using ARE the
 correct files (I checked and double-checked).
 If anyone has had experience with this kind of error
 message and knows how to resolve it, I'd appreciate
 any input. Thanks much!
 Robyn Ayscue
 rayscue.-at-.hsc.wvu.edu
 kajsicat.-at-.yahoo.com
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