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patrickbryant1 / Umol

Protein-ligand structure prediction
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Predict the protein-ligand structure Error #2

Closed SarahKnapp1 closed 8 months ago

SarahKnapp1 commented 8 months ago

Hello, I am trying to run on the Colab With the Input: ID:1ct9_happy LIGAND: OC(=O)CC(C(=O)O)N SEQUENCE:DDLQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSYLWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLETARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDDPSGRAVGVHQSAYK TARGET_POSITIONS:117,120,144,178 NUM_RECYCLES:3 When I try to run my example I get the error in the Predict the protein-ligand structure section : XlaRuntimeError: RESOURCE_EXHAUSTED: Out of memory while trying to allocate 13608450984 bytes. BufferAssignment OOM Debugging. (I am running on GPU)

Can you help me resolve this problem please?

patrickbryant1 commented 8 months ago

Hi Sarah,

OOM means Out Of Memory. The resources online are limited and you need more RAM. Try to crop the protein sequence around your region of interest (117,120,144,178) and run again. Note that you need to update the target positions and your MSA to match the new cropped sequence.

Hope this helps!