fragments library for starting structures having multiple chains

[sokrypton]

Hi all, I have this question similar to a lot of questions in the previous posts. But I still feel a little bit confused after reading some of the replies…

Several modes of Rosetta require fragments library such as loop modeling. Currently, I working with a protein complex which contains 3 identical subunits 322 residues each). This raises several questions:

1. To simulate the whole complex, I need to ask Rosetta to read the whole complex as starting structure.

1) If there are “TER” in the pdb file, the only way to do this is add “read_all_chains” flag, right?
2) If I remove the “TER” in the pdb file, will it still work probably?

2. Since Rosetta require fragment library,

1)how do I generate this library of the whole complex? I used the Robetta server to generate my library, but when uploading the fasta file, it didn’t recognize the trimer complex (322 residues each) instead of a single chain protein (966 residues).
2)So if I use the 966 residues fragment library, will Rosetta still do the modeling correctly?

Any helpful idea will be deeply appreciated!
Thanks a lot!

[sokrypton]

And I just found out that there is an option called “-multi_chain”. Does that have anything to do with the modeling of a complex?

> Hi all, I have this question similar to a lot of questions in the previous posts. But I still feel a little bit confused after reading some of the replies…
>
> Several modes of Rosetta require fragments library such as loop modeling. Currently, I working with a protein complex which contains 3 identical subunits 322 residues each). This raises several questions:
>
> 1. To simulate the whole complex, I need to ask Rosetta to read the whole complex as starting structure.
>
> 1) If there are “TER” in the pdb file, the only way to do this is add “read_all_chains” flag, right?
> 2) If I remove the “TER” in the pdb file, will it still work probably?
>
> 2. Since Rosetta require fragment library,
>
> 1)how do I generate this library of the whole complex? I used the Robetta server to generate my library, but when uploading the fasta file, it didn’t recognize the trimer complex (322 residues each) instead of a single chain protein (966 residues).
> 2)So if I use the 966 residues fragment library, will Rosetta still do the modeling correctly?
>
> Any helpful idea will be deeply appreciated!
> Thanks a lot!

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