N-terminus and loops

[Anonymous]

I am trying to model several loops and the N-terminus of my protein at the same time using the pose-based loop modeling with CCD closure.
This works fine for the loops, but not for the N-terminus, which causes rosetta to crash. From the wiki page:

“Terminal loops can also be specified in a similar fashion, but obviously no chainbreak will be introduced.”

In my loops.txt file I added a line

1 24 0 1

my command line is

rosetta.exe aa 1FOO A -s 1FOO -pose -loops -fold_with_dunbrack -pose_loops_file loops.txt -ex1 -ex2 -fa_input -fa_output

If I just have the N-terminus, rosetta crashes. If I only specify the other (non-terminal) loops, it works.

Is this supposed to work?

Many Thanks,
S.

[Anonymous]

It should not work with Terminal situations

> I am trying to model several loops and the N-terminus of my protein at the same time using the pose-based loop modeling with CCD closure.
> This works fine for the loops, but not for the N-terminus, which causes rosetta to crash. From the wiki page:
>
>
> “Terminal loops can also be specified in a similar fashion, but obviously no chainbreak will be introduced.”
>
> In my loops.txt file I added a line
>
> 1 24 0 1
>
> my command line is
>
> rosetta.exe aa 1FOO A -s 1FOO -pose -loops -fold_with_dunbrack -pose_loops_file loops.txt -ex1 -ex2 -fa_input -fa_output
>
> If I just have the N-terminus, rosetta crashes. If I only specify the other (non-terminal) loops, it works.
>
> Is this supposed to work?
>
> Many Thanks,
> S.

[Anonymous]

Any suggestions how I might still be able to do this?

Many thanks, S.

[bpierce]

You can use the peptide extension protocol to model termini. It is described in Sood & Baker (2006). There is also documentation in the rosetta++ README and some scripts in the rosetta_scripts/peptide_extension/ directory to help you.

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