npts 64 108 86 # num.grid points in xyz
gridfld 1QZQ.maps.fld # grid_data_file
spacing 0.375 # spacing(A)
receptor_types A C H HD N OA SA # receptor atom types
ligand_types A C HD N NA OA SA S # ligand atom types
receptor 1QZQ.pdbqt # macromolecule
gridcenter 22.346 107.315 207.808 # xyz-coordinates or auto
smooth 0.5 # store minimum energy w/in rad(A)
map 1QZQ.A.map # atom-specific affinity map
map 1QZQ.C.map # atom-specific affinity map
map 1QZQ.HD.map # atom-specific affinity map
map 1QZQ.NA.map #atom-specific affinity.map
map 1QZQ.N.map # atom-specific affinity map
map 1QZQ.OA.map # atom-specific affinity map
map 1QZQ.SA.map # atom-specific affinity map
map 1QZQ.S.map # atom-specific affinity.map
elecmap 1QZQ.e.map # electrostatic potential map
dsolvmap 1QZQ.d.map # desolvation potential map
dielectric -0.1465 # 0, constant
Here I have added the map for S file as per instruction from research gate but not got my result.
Still showing error autodock4 I,m sorry I can't find or open "1QZQ.S.map"
is the file "1QZQ.S.map" in the same folders where the other maps are?
Nothing special I could see from the file.
Faced with the same case, I would:
1) check if the file is present in the appropriate directory.
2) See the file content. They are just regular files that can be seen with "more" command or opened though text editors such as gedit.
3) see the output from the autogrid file that generated the map. This might give indications.
It is because of not having the file in same folder... Keep all the files as well as executable files in a single folder and run the docking.....
As per my knowledge, Autogrid program creates .map files depending on the type of atoms present in your ligand molecule. If it fails to create any of .map file then i think you should prepare your ligand with proper orientations.
Anwesh made an excellent point = use scripts! prepare_dpf4.py a bloody old python script automatically generates a docking parameter file of matching map files to your ligand. Depending on the version of AutoDock4 vs 4.2 you might have to take out the unbound_model option but it works if it generates the file. Don't mess with Python 2.5 even though you want to keep 3.6. The scripts come with mglTools packages. prepare_dpf4.py -l -r -p ga_run=10. -p is for parameters. it seems this software having a hard time keeping up with modern technology to the point of obfuscation.
may be check the name of your ligand if it long you face this problem. I got this problem and fix this way.
Using the prepare_dpf4.py script to prepare the docking parameter file. I have faced this problem of "cannot find or open a given map file" even when that very map file was created within the folder. The way around is is as Mr. Aweke Mulu suggests above, rename the ligand and or receptor with a shorter name. Something like Lig1543 or Receptor. It worked for me.
Could you please guide how to prepare_dpf4.py script to produce a parameter file within the working directory.
I would add to Dalal Z. Husein that before saving an output file .gpf, the Molecule should be "opened" not "chosen". Currently, I am doing covalent docking, and in my case, I had to "Open" Molecule under the Grid tab. PS: I am using the GUI AutoDockTools
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