ADL: can't find or open *.receptor.C.map

Bernhard Knapp bernhard.knapp at meduniwien.ac.at
Tue Jan 22 03:39:19 PST 2008


is it possible that there is a problem in the prepare_gpf4.py script? 
because i restartet it a few times with ligand_types="X", where X is 
always an other needed type. by this way i could create all the 
necessary complexLLFGAPVYV.receptor.X.map files and start autodock. if i 
set ligand_types to "A C H OA N S" i does not work. but the problem in 
this solution is that autodock thinks that only one atom type is 
existing in the ligand (written to the *.gpf file, which is created 
without seg fault) this may lead to wrong docking results ...

is there a way of simply using the autodock scoring function as 
described in (Huey et al., 2007) on a given fixed receptor/ligand 
conformation (without any screening of spatial space or ligand flexibility)?


cheers

Bernhard

 


Huey,R., Morris,G.M., Olson,A.J., and Goodsell,D.S. (2007). A 
semiempirical free energy force field with charge-based desolvation. J 
Comput Chem. 28, 1145-1152.

 





Sargis Dallakyan wrote:

>>if I simply add 
>>"map hsg1.SA.map"
>>to the gpf file it says "ERROR: Too many "map" keywords (2); the "types" 
>>command declares only 1 maps."
>>
>>if i change the map line to "map hsg1.SA.map" it complains with
>>"I'm sorry; I can't find or open  "complexLLFGAPVYV.receptor.C.map"
>>    
>>
>
>Sorry for the confusion. "map hsg1.SA.map" should be added if you add a ligand 
>type explicitly to .gpf file. I was thinking that your problem is similar to 
>Monica's problem when I posted and hsg1 is an example used for debugging.
>
>  
>
>>also if i remove the SA from  the "-p ligand_types="A C Cl H F OA N P S 
>>Br NA SA HD"" it does not help and it still says "I cant find or open 
>>"complexLLFGAPVYV.receptor.N.map""
>>
>>what am I doing wrong?
>>    
>>
>
>In your case, something else is causing a problem, since you used 
>prepare_gpf4.py which adds "map *.*.map" lines automatically.
>
>  
>
>>>>/home/bknapp/MGLTools-1.4.6/share/bin/pythonsh 
>>>>/home/bknapp/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py 
>>>>-o complexLLFGAPVYV.gpf -l complexLLFGAPVYV.ligand.pdbqt -r 
>>>>complexLLFGAPVYV.receptor.pdbqt -p ligand_types="A C Cl H F OA N P S Br 
>>>>NA SA HD" -p gridcenter="grid center coordinates" -p npts="grid points"
>>>>        
>>>>
>
>Instead of "grid center coordinates" and "grid points" use ADT or similar tool 
>to find numeric values for these parameters (e.g. npts="60 60 60"). You can use 
>'auto' for gridcenter in which case autogrid will use the center of the 
>macromolecule.
>
>There is recent thread about a bug in prepare_gpf4.py. If you type 
>gridcenter="2.5 6.5 -7.5" you might end up with
>gridcenter 2.5                      # xyz-coordinates or auto
>in your .gpf instead of
>gridcenter 2.5 6.5 -7.5             # xyz-coordinates or auto
>
>Add the missing numbers with a text editor if this is the case.
>
>  
>
>>>>/home/bknapp/downloads/autoDock_4/i86Linux2/autogrid4 -p 
>>>>complexLLFGAPVYV.gpf -l complexLLFGAPVYV.glg
>>>>        
>>>>
>
>Do you get segmentation fault after this step? If not, type
>more complexLLFGAPVYV.gpf
>or run autogrid4 without "-l complexLLFGAPVYV.glg" to monitor the progress.
>
>-Sargis
>________________________________________________
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>
>
>  
>




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