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
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
Yeah i redid the fragment files. The command line I gave for single chain was just an example of what syntax I used. they are not actually what I entered for single chain. I did single chain modeling weeks ago, so I don't have my commands easily accesible, however I can look it up if it'll help. The commands I gave are what I used for multi chain.
Thanks for your help.
Sonya
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