Alphafold2 Colab

Question

[Preeti]

what to do when alphafold2 colab says Runtime disconnected in middle of a structure prediction

[GenoMax]

See if this thread applies in your case: https://stackoverflow.com/questions/57113226/how-can-i-prevent-google-colab-from-disconnecting#:~:text=The%20following%20describes%20the%20conditions,its%20instance%20is%20automatically%20terminated.

[dthorbur]

Are you using the free Colab GPUs or are you connecting to a private one? If it's not related to what GenoMax suggested, in my experience, the free ones can be a little unstable and do sometimes disconnect seemingly at random. I've also noticed with longer sessions, there appears to be a memory leak somewhere in that pipeline and VMs crash if multiple long complexes are run in succession.

How long is the protein/complex you are trying to fold? You may be running out of vRAM if the sequence is too long. ~2400 is the longest I've been able to fold on an NVIDIA T4.

Please provide more information with your questions in the future. It's hard to provide more support with just speculation on our end.