ADL: can't find or open *.receptor.C.map
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
> 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.
>>>-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
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.
>>>complexLLFGAPVYV.gpf -l complexLLFGAPVYV.glg
Do you get segmentation fault after this step? If not, type
or run autogrid4 without "-l complexLLFGAPVYV.glg" to monitor the progress.
More information about the autodock