The total length of multimer sequences is too long

[EricCCLiang]

Dear AlphaLink2 developers,

I'm trying to use AlphaLink2 on a large protein complex. At the "Generate MSAs and templates with MMseqs2" step on ColabFold, I got the following message.

--> 120 raise ValueError(f'The total length of multimer sequences is too long: '
121 f'{total_multimer_length}, while the maximum is '
122 f'{max_multimer_length}. Please use the full AlphaFold '

ValueError: The total length of multimer sequences is too long: 3367, while the maximum is 3000. Please use the full AlphaFold system for long multimers.

Is the limit of the length intrinsic with the UniFold in ColabFold? When installing on HPC, is there parameters we need to tweak for it to work?

Thanks a lot!
Eric

[lhatsk]

Yes, that is only related to ColabFold. How much GPU memory do you have? I think you will need 80GB. You will likely need to use the flash-attention branch, see the install flash-attention section in the README. I just brought the branch up-to-date (not tested though).

[EricCCLiang]

Thanks a lot! I've asked our IT department to install Alphalink2 on our cluster.