Reply To: Loop modeling with multiple chains

[Anonymous]

Loop modeling needs to read in fragment file.Did you change the fragment file when you switched from one chain to multi-chains?Because, obviously the sequence will be different in this case.

> 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