Reply To: Loop modeling with multiple chains

[Anonymous]

I got it to work with multiple chains, with only one region in the loops file instead of two as I was trying earlier. My proteins a homodimer with four chains (chain A&B make one monomer, chain C&D make the other). I was trying earlier to sample two identical regions, one in B and the in D. This was giving the error I mentioned. I broke it down to just one monomer, with two instead of 4 chains and sampling only one region. This worked fine with the syntax I mentioned earlier.
This should work enough for me, although the error does seem odd.

Thanks for looking at my problem.
Sonya

> Hi,
>
> Is it possible in rosetta to model loops for a multi chain protein.
>
> This is the command I run for a single c hain protein:
>
> rosetta.gcc ee 3bf2 _ -relax -looprlx -s 3bf3.pdb -loop_file 3bf2_.loops -loop_model -nstruct 5 > ee3bf3.log
>
> This works. Now, if I have multiple c hains, can I do this:
>
> rosetta.gcc ee 3bf2 _ -relax -looprlx -s 3bf3.pdb -loop_file 3bf2_.loops -loop_model -read_all_chains -nstruct 5 > ee3bf3.log
>
> I tried it, and in the output file while making the first structure, it outputted, indefinetly many times:
>
> 1069900000 tries in choose_fragment_pose
>
> The number in the above “error” kept increasing. It never stops doing this till I hit ctrl-C.
>
> Is is possible to do mulitple chains? Am I using the proper syntax? Do I need to remove chain IDs, TER commands and/or start residues/atoms from 1?
> My fasta file used to make fragments is the entire sequence, with nothing to seperate the chains.
>
> Thanks,
> Sonya