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

Sargis Dallakyan sargis at scripps.edu
Mon Jan 21 10:27:13 PST 2008


> 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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