dockcheck.py atomindex = waterdata[i,0] out of bounds

mirix commented 5 years ago

Hi,

I receive the following error when running WaterDock2

File "/home/mirix/Downloads/WaterDock-2.0/waterdock2.py", line 59, in dockcheck.main(proteinfile, ligandfile) File "/home/mirix/Downloads/WaterDock-2.0/dockcheck.py", line 114, in main atomindex = waterdata[i,0] IndexError: index 9 is out of bounds for axis 0 with size 9

A placedwaters.pdb file with 105 atoms is produced but not a predictedwaters.pdb file.

Best,

Miro

mirix commented 5 years ago

Ok, the problem is that I included crystallographic waters along with my ligand. If I remove them, the program runs smoothly.

Which makes me wonder, what happens if one has one ligand plus one cofactor?

mirix commented 5 years ago

I am using QVina instead of Vina. It is significantly faster.

bigginlab commented 5 years ago

Thanks for this email - that is very useful to note.

Phil

On 13 Dec 2018, at 08:19, mirix notifications@github.com<mailto:notifications@github.com> wrote:

I am using QVina instead of Vina. It is significantly faster.

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dockcheck.py atomindex = waterdata[i,0] out of bounds #1