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

[mirix]

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]

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]

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

[bigginlab]

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. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#1 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/APMck5aRp2QYNAwiHIG3kNsU1C0adADVks5u4eNmgaJpZM4ZPF4w>.

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