flexible backbone design with multiple chains

[Anonymous]

I don’t mean to beat the same drum over an over again, but the issue with designing a non-monomeric protein with a flexible backbone is important. There are two parts to my question.

Firstly, is the mvbb option in rosetta even able to handle a pdb with two chains? Even if I somehow force rosetta to run, will the results be dependable?

Secondly, is it possible to get a fragment file that contains 2 separate chains? Submitting two chains to the fragment server produces fragment files for 1 chain that has the combined sequences of the two original chains. If that is not possible, is there any way to get rosetta to accept 4 fragment files rather than two (by modifying the paths.txt file for example) so that it will design two separate chains at the same time?

I actually used the following command to run a design on a dimer with 600 total residues:
rosetta.osx aa ABCD _ -s ABCD_ideal.pdb -design -mvbb -multi_chain -resfile ABCD.rrf

The result was a pdb file where the two separate chains had a peptide bond between them (I assume this occurred due to the problem with the fragment files I mentioned above). Assuming the other problems are solved, is the command I used correct or is, for example, ‘-read_all_chains’ better than ‘-multi_chain’ in this situation.

Thanks a lot for the help.

[sokrypton]

Hi lesi,

It’s good to see your post! I have the same problem and questions. I met the same “multi chains” problem when I am using the loop mode. I saw one of the previous post said that you need to upload the sequences of all chains as one chain. But it is really odd to me, and I don’t know how to make sure the rosetta will work properly when you feed it with the hugh “multi chain fragment library”.

And in my case, neither the “real_all_chains” nor the “multi_chain” options worked, maybe because that rosetta mode doesn’t support multi chain simulation. In fact, it seems that only the docking mode can yield some result with separated chains.

I’m sorry that I can’t answer any of your quesitions. I just hope someone will have a good idea if it is a common problem.

-Yizhou

> I don’t mean to beat the same drum over an over again, but the issue with designing a non-monomeric protein with a flexible backbone is important. There are two parts to my question.
>
> Firstly, is the mvbb option in rosetta even able to handle a pdb with two chains? Even if I somehow force rosetta to run, will the results be dependable?
>
> Secondly, is it possible to get a fragment file that contains 2 separate chains? Submitting two chains to the fragment server produces fragment files for 1 chain that has the combined sequences of the two original chains. If that is not possible, is there any way to get rosetta to accept 4 fragment files rather than two (by modifying the paths.txt file for example) so that it will design two separate chains at the same time?
>
> I actually used the following command to run a design on a dimer with 600 total residues:
> rosetta.osx aa ABCD _ -s ABCD_ideal.pdb -design -mvbb -multi_chain -resfile ABCD.rrf
>
> The result was a pdb file where the two separate chains had a peptide bond between them (I assume this occurred due to the problem with the fragment files I mentioned above). Assuming the other problems are solved, is the command I used correct or is, for example, ‘-read_all_chains’ better than ‘-multi_chain’ in this situation.
>
> Thanks a lot for the help.
>

[Anonymous]

Hi, did you use rosettadock 2.3 or rosettadock 3.0? I am curious.

> I don’t mean to beat the same drum over an over again, but the issue with designing a non-monomeric protein with a flexible backbone is important. There are two parts to my question.
>
> Firstly, is the mvbb option in rosetta even able to handle a pdb with two chains? Even if I somehow force rosetta to run, will the results be dependable?
>
> Secondly, is it possible to get a fragment file that contains 2 separate chains? Submitting two chains to the fragment server produces fragment files for 1 chain that has the combined sequences of the two original chains. If that is not possible, is there any way to get rosetta to accept 4 fragment files rather than two (by modifying the paths.txt file for example) so that it will design two separate chains at the same time?
>
> I actually used the following command to run a design on a dimer with 600 total residues:
> rosetta.osx aa ABCD _ -s ABCD_ideal.pdb -design -mvbb -multi_chain -resfile ABCD.rrf
>
> The result was a pdb file where the two separate chains had a peptide bond between them (I assume this occurred due to the problem with the fragment files I mentioned above). Assuming the other problems are solved, is the command I used correct or is, for example, ‘-read_all_chains’ better than ‘-multi_chain’ in this situation.
>
> Thanks a lot for the help.
>

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