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ccsb-scripps / AutoDock-Vina

AutoDock Vina
http://vina.scripps.edu
Apache License 2.0
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Dry.py error when running an hydrated docking (Autodock) #157

Closed afsp22 closed 1 year ago

afsp22 commented 1 year ago

Hi everyone! I'm trying to run an hydrated docking protocol. In the last step, I've to run dry.pt using the command: $ python dry.py -c -r protein.pdbqt -m protein.W.map -i ligand_HYDRO_protein.dlg

but I'm getting this error message:

File "dry.py", line 1184, in grid = getmap(grid) File "dry.py", line 690, in getmap data = array(data, 'f').reshape(pts[2], pts[1], pts[0]) TypeError: 'float' object cannot be interpreted as an index

I tried to replace the pts[i] by int(pts[i]), but now I have a different error message:

File "dry.py", line 1194, in harvest, affinity = getpoints(grid, coord(w), distance = 1.0) # angstroms File "dry.py", line 739, in getpoints harvesting.append( data[z,y,x] ) IndexError: index 41 is out of bounds for axis 0 with size 41

Can someone help me solve this issue? Thank you very much!

domiko96 commented 1 year ago

Exactly the same problem here. Did you ever solve this?

domiko96 commented 1 year ago

Seems like various people run into this, see https://github.com/ccsb-scripps/AutoDock-Vina/issues/82 Maybe it is a numpy / python environment issue. Somebody reported to be able to run it via anaconda. I tried this as well with no luck

diogomart commented 1 year ago

Fixed in #202. Thanks @domiko96 :+1: